Miracle-dz/UniFAR-FTUs huggingface dataset:
The Sociology of Cities

This publication examines the urbanization process, the structure of urban regions, the internal structure of cities, and social consequences and responses to urbanization. It weaves the major theoretical perspectives - human ecology, critical/neo-Marxian and social psychology - throughout the text. It includes cross-cultural material and a chapter on urbanization in the less developed world.
Improving nonparameteric Bayesian inference: experiments on unsupervised word segmentation with adaptor grammars

One of the reasons nonparametric Bayesian inference is attracting attention in computational linguistics is because it provides a principled way of learning the units of generalization together with their probabilities. Adaptor grammars are a framework for defining a variety of hierarchical nonparametric Bayesian models. This paper investigates some of the choices that arise in formulating adaptor grammars and associated inference procedures, and shows that they can have a dramatic impact on performance in an unsupervised word segmentation task. With appropriate adaptor grammars and inference procedures we achieve an 87% word token f-score on the standard Brent version of the Bernstein-Ratner corpus, which is an error reduction of over 35% over the best previously reported results for this corpus.
Simultaneous Wireless Information and Power Transfer in MISO Full-Duplex Systems

This paper investigates a multiuser multiple-input single-output (MISO) full-duplex (FD) system for simultaneous wireless information and power transfer (SWIPT), in which a multi-antenna base station (BS) simultaneously sends wirelessly information and power to a set of single-antenna mobile stations (MSs) using power splitters (PSs) in the downlink and receives information in the uplink in FD mode. In particular, we address the joint design of the receive PS ratio and the transmit power at the MSs, and the beamforming matrix at the BS under signal-to-interference-plus-noise ratio (SINR) and the harvested power constraints. Using semidefinite relaxation (SDR), we obtain the solution to the problem with imperfect channel state information (CSI) of the self-interfering channels. Furthermore, we propose another suboptimal zero-forcing (ZF) based solution by separating the optimization of the transmit beamforming vector and the PS ratio. Simulation results are provided to evaluate the performance of the proposed beamforming designs.
Novel dimeric structure of phage ϕ29-encoded protein p56: insights into uracil-DNA glycosylase inhibition

Protein p56 encoded by the Bacillus subtilis phage ϕ29 inhibits the host uracil-DNA glycosylase (UDG) activity. To get insights into the structural basis for this inhibition, the NMR solution structure of p56 has been determined. The inhibitor defines a novel dimeric fold, stabilized by a combination of polar and extensive hydrophobic interactions. Each polypeptide chain contains three stretches of anti-parallel β-sheets and a helical region linked by three short loops. In addition, microcalorimetry titration experiments showed that it forms a tight 2:1 complex with UDG, strongly suggesting that the dimer represents the functional form of the inhibitor. This was further confirmed by the functional analysis of p56 mutants unable to assemble into dimers. We have also shown that the highly anionic region of the inhibitor plays a significant role in the inhibition of UDG. Thus, based on these findings and taking into account previous results that revealed similarities between the association mode of p56 and the phage PBS-1/PBS-2-encoded inhibitor Ugi with UDG, we propose that protein p56 might inhibit the enzyme by mimicking its DNA substrate.
Progress toward virtual screening for drug side effects

The development and application of a computational protocol for conducting virtual screens of drug side interactions is described. A conventional drug‐docking algorithm (AutoDock) is used to conduct two separate studies. First, a series of docking simulations is performed by using guanosine diphosphate and adenosine diphosphate as prototype drugs with the goal of successfully differentiating known receptors from a large number of bait receptors. Using the electrostatic energy of the purine ring as a basis for discrimination allows the correct identification of receptors in blind studies with 100% specificity and 94% sensitivity. In a second study, similar methodology is used to investigate the binding of clinically relevant inhibitors (Gleevec, purvalanol A, and hymenialdisine) to a variety of protein kinase targets. Overall, excellent agreement between experimental and predicted preferences for kinase targets is obtained. An important conclusion from the latter study is that homology‐modeled structures of putative receptors may reasonably be used as targets for docking when directly solved crystal structures are not available. The prospects for routine application of the methodology as a means of identifying potential side interactions of candidate drugs are discussed. Proteins 2002;48:664–671. © 2002 Wiley‐Liss, Inc.
Reply to the letter ‘A brief comment about predictive models for mortality in intensive care units’

We have with interest read the comments by Palaz on-Bru and colleagues regarding our recently published manuscript entitled ‘Development and internal validation of the Simplified Mortality Score for the Intensive Care Unit (SMS-ICU)’, including the response to our discussion of their intensive care unit (ICU) mortality risk score. As outlined, we chose to use data from observational studies and randomised clinical trials (RCTs) for the development of the SMS-ICU. Limitations of this approach, including clinical heterogeneity, have been discussed in our manuscript. Strengths of using data from large international observational studies and pragmatic RCTs include high external validity (generalisability), high data quality owing to the prospective data collection and monitoring, and limited risk of inflated estimates, as compared to single-centre studies, which need to be interpreted with caution. Palaz on-Bru et al. argue that treatment effects in the RCTs could affect our model. However, the intervention in two of the three RCTs had no effect on mortality, and for the last RCT, a pre-planned sensitivity analysis excluding the intervention group was conducted without affecting model performance. Consequently, the risk of treatment effect in the included RCTs is limited if present at all. Regarding the outcome of interest, we chose a long-term fixed-time mortality outcome as recommended. Very few patients stay in the ICU for more than 90 days, and in those who do, clinical prediction rules perform less well. Importantly, in-ICU and in-hospital mortality are considered inferior outcomes as they are affected by discharge practices. We decided a priori to use all available data to develop the model to ensure sufficient power, and to plan external validation in a sample that allows us to assess temporal generalisability as well. Regarding the events per variable (EPV), the rule-of-thumb recommending ≥ 10 EPV for sufficient power relates to the number of variables assessed during model derivation, and not on the number of variables included in the final model. With 12 variables assessed in Palaz onBru et al.’s model, the EPV is 7.5 (and not 15), whereas the corresponding EPV is 64 in SMSICU. Importantly, an EPV ≥ 10 is a simplified rule-of-thumb, and the risk of overfitting depends on the modelling strategy and the total number of degrees of freedom and models assessed, and a model with ≥ 10 EPV may still be substantially underpowered. We agree that it is up to clinicians, administrators and researchers to judge which model best fits their needs, however, methodological rigour, including adequate power, internal validation and high external validity are prerequisites when developing clinical prediction rules.
EVALUATION OF BACK-OFF ALGORITHM PERFORMANCE OF MAC LAYER IEEE 802.11 WLAN

The medium access control (MAC) protocol is the main element which determines the system throughput in wireless local area networks. The MAC technique of the IEEE 802.11 protocol is called Distributed Coordination Function (DCF). However, in the DCF access procedure, the system throughput decreases when the number of stations is large. This paper proposes a simple and effective contention window-resetting scheme, named Double Increment Double Decrement (DIDD), to improve the performance of IEEE 802.11 Binary Exponential Backoff (BEB) under an error-prone environment. Our work becomes important and meaningful in the sense that it predicts both IEEE 802.11 BEB and DIDD performance very accurately considering transmission errors. We explore the effect of transmission errors; packet size, data rate and network size on the performance of BEB and DIDD, in terms of throughput efficiency, average packet delay, packet drop probability and packet inter arrival time.
Efficient Isolation of Pure and Functional Mitochondria from Mouse Tissues Using Automated Tissue Disruption and Enrichment with Anti-TOM22 Magnetic Beads

To better understand molecular mechanisms regulating changes in metabolism, as observed e.g. in diabetes or neuronal disorders, the function of mitochondria needs to be precisely determined. The usual isolation methods such as differential centrifugation result in isolates of highly variable quality and quantity. To fulfill the need of a reproducible isolation method from solid tissues, which is suitable to handle parallel samples simultaneously, we developed a protocol based on anti-TOM22 (translocase of outer mitochondrial membrane 22 homolog) antibody-coupled magnetic beads. To measure oxygen consumption rate in isolated mitochondria from various mouse tissues, a traditional Clark electrode and the high-throughput XF Extracellular Flux Analyzer were used. Furthermore, Western blots, transmission electron microscopic and proteomic studies were performed to analyze the purity and integrity of the mitochondrial preparations. Mitochondrial fractions isolated from liver, brain and skeletal muscle by anti-TOM22 magnetic beads showed oxygen consumption capacities comparable to previously reported values and little contamination with other organelles. The purity and quality of isolated mitochondria using anti-TOM22 magnetic beads was compared to traditional differential centrifugation protocol in liver and the results indicated an obvious advantage of the magnetic beads method compared to the traditional differential centrifugation technique.
SimTag: Exploiting tag bits similarity to improve the reliability of the data caches

Though tag bits in the data caches are vulnerable to transient errors, few effort has been made to reduce their vulnerability. In this paper, we propose to exploit prevalent same tag bits to improve error protection capability of the tag bits in the data caches. When data are fetched from the main memory, it is checked if adjacent cache lines have the same tag bits as those of the data fetched. This similarity information is stored in the data caches as extra bits to be used later. When an error is detected in the tag bits, the similarity information is used to recover from the error in the tag bits. The proposed scheme has small area, energy, and performance overheads with error protection coverage of 97.9% on average. In contrast, the previously proposed In-Cache Replication scheme is shown to incur large performance and energy overheads.
Diversity in Antistaphylococcal Mechanisms among Membrane-Targeting Antimicrobial Peptides

ABSTRACT Many antimicrobial peptides permeabilize the bacterial cytoplasmic membrane. However, it is unclear how membrane permeabilization and antimicrobial activity are related for distinct peptides. This study investigated the relationship between Staphylococcus aureusmembrane permeabilization and cell death due to the following antistaphylococcal peptides: thrombin-induced platelet microbicidal protein 1 (tPMP-1), gramicidin D, and protamine. Isogenic S. aureus strains ISP479C and ISP479R (tPMP-1 susceptible and resistant, respectively), were loaded with the fluorochrome calcein and exposed to a range of concentrations of each peptide. Flow cytometry was then used to monitor membrane permeabilization by quantifying the release of preloaded calcein. Killing was determined by quantitative culture at time points simultaneous to measurement of membrane permeabilization. Membrane permeabilization and killing caused by tPMP-1 occurred in a time- and concentration-dependent manner, reflecting the intrinsic tPMP-1 susceptibilities of ISP479C and ISP479R. In comparison, gramicidin D killed both S. aureusstrains to equivalent extents in a concentration-dependent manner between 0.5 to 50 μg/ml, but cell permeabilization only occurred at the higher peptide concentrations (25 and 50 μg/ml). Protamine permeabilized, but did not kill, either strain at concentrations up to 10 mg/ml. Regression analyses revealed different relationships between membrane permeabilization and staphylocidal activity for the distinct antimicrobial peptides. Taken together, these findings demonstrate that permeabilization, per se, does not invariably result in staphylococcal death due to distinct antimicrobial peptides. Thus, although each of these peptides interacts with the S. aureus cytoplasmic membrane, diversity exists in their mechanisms of action with respect to the relationship between membrane permeabilization and staphylocidal activity.
conf/cse/NigusseDN09 conf/dbsec/VerslypeDNNLV08 Girma Nigusse = Girma Enideg Nigusse Privacy Codes of Practice for the Social Web: The Analysis of Existing Privacy Codes and Emerging Social-Centric Privacy Risks

Privacy codes of practice developed in the 1980s in response to the concerns about the introduction of computerized databases, automated personal information processing systems, and easy transmission of personal information across national and international boundaries. The current data-practice guidelines, laws, and model-codes have been modeled based on these early codes. Starting from the early 2000, the socialization of the Web introduced a new kind of private information flow model and new privacy risks. In this paper, we analyzes the core principles of existing privacy codes with respect to emerging social-centric privacy risks. Our major contribution in this work is twofold. Legally - this evaluation is useful to enhance current privacy codes for the Social Web. Technically - this evaluation is useful to design the future social-centric privacy policy languages and their data handling specifications.
Zero Phase speech representation for robust formant tracking

In this paper we present a speech representation based on the Linear Predictive Coding of the Zero Phase version of the signal (ZP-LPC) and its robustness in presence of additive noise for robust formant estimation. Two representations are proposed for using in the frequency candidate proposition stage of the formant tracking algorithm: 1) the roots of ZP-LPC and 2) the peaks of its group delay function (GDF). Both of them are studied and evaluated in noisy environments with a synthetic dataset to demonstrate their robustness. Proposed representations are then used in a formant tracking experiment with a speech database. A beam search algorithm is used for selecting the best candidates as formant. Results show that our method outperforms related techniques in noisy test configurations and is a good fit for use in applications that have to work in noisy environments.
Robust near-separable nonnegative matrix factorization using linear optimization

Nonnegative matrix factorization (NMF) has been shown recently to be tractable under the separability assumption, under which all the columns of the input data matrix belong to the convex cone generated by only a few of these columns. Bittorf, Recht, Re and Tropp ('Factoring nonnegative matrices with linear programs', NIPS 2012) proposed a linear programming (LP) model, referred to as Hottopixx, which is robust under any small perturbation of the input matrix. However, Hottopixx has two important drawbacks: (i) the input matrix has to be normalized, and (ii) the factorization rank has to be known in advance. In this paper, we generalize Hottopixx in order to resolve these two drawbacks, that is, we propose a new LP model which does not require normalization and detects the factorization rank automatically. Moreover, the new LP model is more flexible, significantly more tolerant to noise, and can easily be adapted to handle outliers and other noise models. Finally, we show on several synthetic data sets that it outperforms Hottopixx while competing favorably with two state-of-the-art methods.
Kill kinetics and regrowth patterns of Escherichia coli exposed to gentamicin concentration-time profiles simulating in vivo bolus and infusion dosing

The relative influence of peak concentration (Cmax) versus the area under the antibiotic concentration-time curve (AUC) on the bactericidal effect of gentamicin against Escherichia coli NCTC 10418 was studied. Bacteria in the lag phase were exposed to an in vitro gentamicin concentration series which mirrored the concentrations determined in patients after 80-mg intravenous bolus (1 min) and 80-mg intravenous infusion (30 min) doses. Bacterial viable cell counts and gentamicin concentrations were measured before and during antibiotic exposure. Both the Cmax and AUC were shown to be factors determining antibacterial activity; however, the Cmax was an independent determinant of effect. These findings indicate that bolus intravenous dosing with gentamicin could maximize bactericidal activity. Increased efficacy could result at any given daily antibiotic dose if delivered via bolus with long intervals (12 to 24 h) between doses if appropriate precautions to avoid toxicity are taken.
The complexity of theorem-proving procedures

It is shown that any recognition problem solved by a polynomial time-bounded nondeterministic Turing machine can be “reduced” to the problem of determining whether a given propositional formula is a tautology. Here “reduced” means, roughly speaking, that the first problem can be solved deterministically in polynomial time provided an oracle is available for solving the second. From this notion of reducible, polynomial degrees of difficulty are defined, and it is shown that the problem of determining tautologyhood has the same polynomial degree as the problem of determining whether the first of two given graphs is isomorphic to a subgraph of the second. Other examples are discussed. A method of measuring the complexity of proof procedures for the predicate calculus is introduced and discussed.
Beyond information extraction: The role of ontology in military report processing

Information extraction tools like SMES transform natural language into formal representation, e.g. into feature structures. Doing so, these tools exploit and apply linguistic knowledge about the syntactic and morphological regularities of the language used. However, these tools apply semantic as well as pragmatic knowledge only partially at best. Automatic processing of military reports has to result in a visualization of the reports content by map as well as in an actualization of the underlying database in order to allow for the actualization of the common operational picture. Normally, however, the information provided by the result of the information extraction is not explicit enough for visualization processes and database insertions. This originates from the reports themselves that are elliptical, ambiguous, and vague. In order to overcome this obstacle, the situational context and thus semantic and pragmatic aspects have to be taken into account. In the paper at hand, we present a system that uses an ontological module to integrate semantic and pragmatic knowledge. The result of the completion contains all the specifications to allow for a visualization of the report’s content on a map as well as for a database actualization.
Typology of business relationships using buyers' and suppliers' perceptions

This paper focuses on the perception of the business relationship values in a dyadic approach. An overview of the related literature provides a good basis for conceptualization. The Integrated Business Relationship Value Model was chosen as a concept of the research; therefore, this paper presents the validation of the constructs of this model using the PLS-SEM software for the sample of 174 respondents. Based on the model, a survey regarding the economic and social values of the relationship was conducted with the supplier and buyer side of the dyads. The results of the analysis provide a description of the perceptions of both sides of the relationship based on the economic and social value constructs. The results also provide a segmentation of the sample based on value perceptions. We found three segments of behavior using the dual perception approach: (1) In “matching segment” relationships, the perception of the relationship is similar on the both sides; (2) In “happy supplier segment” relationships, the perceptions are different, and the relationship is more valuable for the supplier; (3) In “happy buyer segment” relationships, the relationship is more valuable for the buyer. This article contributes both the conceptualization and the typology of dyadic relationships. The results show that approximately 48 percent of the investigated relationships are mismatched, which indicates a need for greater focus on the evaluation of relationships in practical business management processes.
Design and Calibration of a Novel Camera-Based Bio-Inspired Polarization Navigation Sensor

The remarkable ability of animals using the skylight polarization pattern provides a significant inspiration for the autonomous robotic navigation. The bio-inspired polarization navigation approach with advantages of efficiency and reliability has aroused much interesting for experts to perform further research. The sensor of measuring the skylight polarization pattern plays a key role in bio-inspired polarization navigation. A novel camera-based bionic polarization navigation sensor is designed and implemented. We propose a robust measurement method based on the least squares by utilizing all outputs of measurement units. For improving the precision of measurement, the errors of sensor are analyzed, and an effective calibration algorithm is proposed in detail. The experiment results show that the measurement accuracy is improved greatly after calibration. Finally, to evaluate the performance of our sensor, experiments of measuring the actual skylight polarization pattern are performed and compared with the results from the single-scattering Rayleigh theory. The comparison results indicate that our sensor can achieve an effective and accuracy measurement in practice.
Leisure Statisfaction and Acculturative Stress: The Case of Chinese-Canadian Immigrants

Abstract The purpose of this study was to examine the causal relationship between leisure satisfaction and acculturative stress. Chinese immigrants to Canada were surveyed six months apart. Four kinds of acculturative stress (all at Time 2) were each hierarchically regressed on: age and gender, years in Canada, the corresponding stressor, and six types of leisure satisfaction (all at Time 1). Results indicated that: (a) social leisure satisfaction lessened loss/nostalgia-based stress; and (b) social, psychological, and aesthetic leisure satisfaction mitigated, while physiological leisure satisfaction exacerbated, perceived discrimination-based stress. These results suggest that, while facilitating certain types of leisure satisfaction (e.g., social) may be beneficial, fostering others (e.g., physiological) could have undesirable consequences.