Miracle-dz/UniFAR-FTUs huggingface dataset:
Flexible DNA bending in HU–DNA cocrystal structures

HU and IHF are members of a family of prokaryotic proteins that interact with the DNA minor groove in a sequence‐specific (IHF) or non‐specific (HU) manner to induce and/or stabilize DNA bending. HU plays architectural roles in replication initiation, transcription regulation and site‐specific recombination, and is associated with bacterial nucleoids. Cocrystal structures of Anabaena HU bound to DNA (1P71, 1P78, 1P51) reveal that while underlying proline intercalation and asymmetric charge neutralization mechanisms of DNA bending are similar for IHF and HU, HU stabilizes different DNA bend angles (∼105–140°). The two bend angles within a single HU complex are not coplanar, and the resulting dihedral angle is consistent with negative supercoiling. Comparison of HU–DNA and IHF–DNA structures suggests that sharper bending is correlated with longer DNA binding sites and smaller dihedral angles. An HU‐induced bend may be better modeled as a hinge, not a rigid bend. The ability to induce or stabilize varying bend angles is consistent with HU's role as an architectural cofactor in many different systems that may require differing geometries.
Agrin triggers the clustering of raft‐associated acetylcholine receptors through actin cytoskeleton reorganization

Background information. Cholesterol/sphingolipid‐rich membrane microdomains or membrane rafts have been implicated in various aspects of receptor function such as activation, trafficking and synapse localization. More specifically in muscle, membrane rafts are involved in AChR (acetylcholine receptor) clustering triggered by the neural factor agrin, a mechanism considered integral to NMJ (neuromuscular junction) formation. In addition, actin polymerization is required for the formation and stabilization of AChR clusters in muscle fibres. Since membrane rafts are platforms sustaining actin nucleation, we hypothesize that these microdomains provide the suitable microenvironment favouring agrin/MuSK (muscle‐specific kinase) signalling, eliciting in turn actin cytoskeleton reorganization and AChR clustering. However, the identity of the signalling pathways operating through these microdomains still remains unclear.
Rate bounded linear parameter varying control of a wind turbine in full load operation

Abstract This paper considers the control of wind turbines using an LPV design technique. The controller design is done by a combination of a method that uses elimination of controller variables and a method using a congruent transformation followed by a change of variables. An investigation is performed to understand the gap between zero rate of variation and arbitrary fast rate of variation for the selected scheduling variable. In particular it is analysed for which rate of variation, the local performance level starts to deteriorate from the performance level that can be obtained locally by LTI controllers. A rate of variation is selected which is expected only to be exceeded outside the normal wind turbine operating conditions. For this rate of variation a controller has been designed and simulations show a performance level over the operating region which is very similar to what can be obtained by LTI designs for the specific operating condition. The LPV controller, however, works for the whole operating range with reasonably fast changes within this.
Modeling Amorphous Ribbons in Energy Harvesting Applications

This paper describes an approach to an electromagnetic harvester exploiting the magnetostrictive properties of amorphous ribbons to generate an electromotive force upon time-varying stresses of vibrational origin. Alloys of composition Fe78B13Si9, thermally treated for maximum magnetic response to tensile stresses, are considered. A compact design is proposed, where the sensing core, a short bundle of few flux-closed amorphous strips subjected to a bias dc field, is connected at one end to a vibrating wall. A finite element calculation of the whole device under different resistive load conditions on the secondary circuit is made. It results into a power around 20 μW/cm3 per unit volume of core material delivered into the load at 100 Hz.
Behavior-based indices for evaluating communities in online social networks

Online Social Network (OSN) users generate massive amounts of information by their online interactions, by publishing profiles and posting content. Detection and analysis of the dense sub-structures of networks, called communities could facilitate a comprehensive understanding of OSNs. This presents the challenge of formulating appropriate means to evaluate and validate each detected community. Most researchers have tackled this issue by comparing results obtained from community detection algorithms with information on available social grouping as a ground-truth. However, social grouping does not guarantee formation or existence of an experienced sense of community, based on the community-oriented behavior patterns of its users. This study presents a new scoring function that targets the behavior of nodes in order to validate detected communities. Indeed, we employ this function as a Cluster Validity Index (CVI) for evaluating detected communities. Then, performance of the proposed CVI was compared with other known functions by ranking in terms of several goodness metrics, on a variety of homogeneous networks. This study also presents an enhanced version of the CVI to evaluate communities efficiently in heterogeneous networks. A number of experiments have been provided to demonstrate the effectiveness and reliability of the proposed CVI for heterogeneous networks.
Phase transition thresholds for some Friedman‐style independence results

We classify the phase transition thresholds from provability to unprovability for certain Friedman‐style miniaturizations of Kruskal's Theorem and Higman's Lemma. In addition we prove a new and unexpected phase transition result for ε0. Motivated by renormalization and universality issues from statistical physics we finally state a universality hypothesis. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Prevalence of vertebral deformities and symptomatic vertebral fractures in corticosteroid treated patients with rheumatoid arthritis.

OBJECTIVE This study was designed to determine whether the prevalence of vertebral deformities in patients with rheumatoid arthritis (RA) treated with corticosteroids (Cs) is higher than in RA patients not receiving Cs therapy. PATIENTS AND METHODS This multicentre cross-sectional study included 205 patients with RA who were receiving Cs orally on a daily basis and 205 patients with RA who did not receive Cs, matched for sex and age. Vertebral deformities were scored according to the Kleerekoper method. RESULTS Vertebral deformities were found in 52 (25%) patients on Cs and in 26 (13%) patients not on Cs. Sixteen (8%) patients in the group on Cs had experienced clinical manifestations of an acute vertebral fracture in the past vs only three patients (1.5%) among those not on Cs. The use of Cs tended to increase the risk of developing a vertebral deformity [adjusted odds ratio (OR) 1.56, 95% confidence interval (CI) 0.81-2.99] and symptomatic vertebral fracture (adjusted OR 1.42, 95% CI 0.24-8.32). Each 1-mg increase in the current daily Cs dose increased the risk of a vertebral deformity (adjusted OR 1.05, 95% CI 0.98-1.13) and of a symptomatic vertebral fracture (adjusted OR 1.05, 95% CI 0.89-1.24). CONCLUSION There is a higher prevalence of vertebral deformities and clinical manifestations of vertebral fractures in patients on Cs than in those not on Cs. Our data indicate that the use of Cs and each 1-mg increase in the current daily Cs dose may increase the risk of development of a vertebral deformity and symptomatic vertebral fracture in patients with RA.
Neutralizing Antibodies Targeted to Mucin-Type Carbohydrate Epitopes of Human Immunodeficiency Virus

The cancer-related mucin-type carbohydrate neoantigen Tn was found on gpl60 and gpl20 of human immunodeficiency virus (HIV). Immunoglobulin G (IgG) and IgM monoclonal antibodies (MAbs) against Tn neutralized infection with cell-free virus and blocked fusion between HIV-infected and uninfected cells. This inhibition was found in infection of both lymphocytic cells and monocytoid cells. Viruses tested included six HIV-1 and five HIV-2 isolates propagated in different cells, as well as infectious plasma from AIDS patients. The antiviral effect of anti-Tn MAbs occurred by specific binding of the MAb to the virus; this binding was inhibitable by pure Tn antigen, and indications were found that this inhibition occurred at a pre-entry step. Boosting the naturally occurring low-titer anti-Tn activity may be of prophylactic value, as suggested by the in vitro neutralization found in this study.
Quiet please, do not disturb: a hypothesis of embryo metabolism and viability.

This review uses nutritional markers of normal and impaired development to address the question; what makes a viable mammalian preimplantation embryo? Resolution of this question is important to ensure the long-term safety of embryo-based biotechnologies in man and domestic animals, the optimisation of embryo production and culture conditions and the development of methods to select viable embryos for replacement. After considering the nutrition of embryos and somatic cells, and the phenomenon of caloric restriction, it is concluded that preimplantation embryo survival is best served by a relatively low level of metabolism; a situation achieved by reducing the concentrations of nutrients in culture media and encouraging the use endogenous resources.
The Chemical Formulary:

AbstractTHESE two volumes consist of numerous receipts for the manufacture of a wide range of materials dealt with under such varying headings as adhesives, alloys and metals, food products, explosives, ceramics, insecticides, plastic materials, etc., to waterproofing of materials. The information used in compiling these books has been obtained from a variety of sources, including industry and patent literature, and has been carefully considered by a board of editors drawn from a large number of educational institutions and industrial firms.The Chemical Formulary: a Condensed Collection of Valuable, Timely, Practical Formulas for making Thousands of Products in all Fields of Industry. Editor-in-Chief: H. Bennett. Vol. 1. Pp. x + 604. Vol. 2. Pp. ix + 570. (London: Chapman and Hall, Ltd., 1933–1935.) 25s. net each vol.
Buttoning down archaeology.

Although there is plethora of material about historical clothing, very little is ever said of the button's used to fasten them. While buttons as collectibles are also well represented in the literature, the emphasis is on the exotic rather than the mundane, with little connection to the garments from which these 'treasures' were derived. This paper initially looks at the main button types likely to be encountered on Australian excavations, with an emphasis on those ordinary buttons which dominate the archaeological repertoire. Further discussion about buttons in the context of an urban environment focuses on eight houses from the CSR site at Pyrmont, excavated in 1996 by Casey & Lowe Associates. To develop our understanding about the 'use' of buttons the paper ends with a discussion about buttons within the context of clothing. It is in the small things that are lost or misplaced that the details of everyday life may be found. Small artefacts from urban excavations relating to everyday and personal activities do not often form a major component of the percentage of artefacts recovered, or figure significantly in the final assessment of the results of the excavation. Buttons found on urban archaeological sites are one example of the small things that are often not considered as having high significance in the final analysis of the social context of a site. Although there is a substantial corpus of material relating to past fashions, and buttons as collectibles, there is little that relates directly to the majority of buttons found on urban archaeological sites.
A novel multimodal gaze-controlled Hindi virtual keyboard for disabled users

Over the last decade, there has been a gradual increase in the number of people with mobility and speech impairments who require novel communication devices. Most of the recent works focus on the Latin script; there is a lack of appropriate assistive devices for scripts that are specific to a country. In this paper, we propose a novel multimodal Hindi language virtual keyboard based on a menu selection with eight commands providing access to spell and type 63 different Hindi language characters along with other functionalities such as the delete command for corrections. The system has been evaluated with eight able-bodied individuals who performed a specially designed typing task. The spelling task has been achieved in three different modalities using: (i) a mouse, (ii) a portable eye-tracker, and (iii) a portable eye-tracker combined with a soft-switch. The performance has been evaluated over the changes that occur with the use of each modality in terms of typing speed and information transfer rate (ITR) at both the command and letter levels for each participant. The average speed across participants with mouse only, eye-tracker only, and eye-tracker with soft-switch were 17.12 letters/min, 10.62 letters/min, and 13.50 letters/min, respectively. The ITRs at the command and letter levels were about 67.58 bits/minute and 62.67 bits/minute, respectively, with only the eye-tracker option. Based on its robustness, the proposed system has the potential to be used as a means of augmentative communication for patients suffering from mobility and speech impairment, and can contribute to substantial improvement in their quality of life.
Imaging of Plasmodium Liver Stages to Drive Next-Generation Antimalarial Drug Discovery

Imidazolopiperazine compounds inhibit liver-stage malaria parasites with one oral dose in mice. Most malaria drug development focuses on parasite stages detected in red blood cells, even though, to achieve eradication, next-generation drugs active against both erythrocytic and exo-erythrocytic forms would be preferable. We applied a multifactorial approach to a set of >4000 commercially available compounds with previously demonstrated blood-stage activity (median inhibitory concentration < 1 micromolar) and identified chemical scaffolds with potent activity against both forms. From this screen, we identified an imidazolopiperazine scaffold series that was highly enriched among compounds active against Plasmodium liver stages. The orally bioavailable lead imidazolopiperazine confers complete causal prophylactic protection (15 milligrams/kilogram) in rodent models of malaria and shows potent in vivo blood-stage therapeutic activity. The open-source chemical tools resulting from our effort provide starting points for future drug discovery programs, as well as opportunities for researchers to investigate the biology of exo-erythrocytic forms.
Social Adjustment, Academic Adjustment, and the Ability to Identify Emotion in Facial Expressions of 7-Year-Old Children

ABSTRACT The authors aimed to examine the possible association between (a) accurately reading emotion in facial expressions and (b) social and academic competence among elementary school-aged children. Participants were 840 7-year-old children who completed a test of the ability to read emotion in facial expressions. Teachers rated children's social and academic behavior using behavioral rating scales. The authors found that children who had more difficulty identifying emotion in faces also were more likely to have more problems overall and, more specifically, with peer relationships among boys and with learning difficulties among girls. Findings suggest that nonverbal receptive skill plays a significant role in children's social and academic adjustment.
TRIP: A Tussle-Resistant Internet Pricing Mechanism

The rapid development of network applications has led to a dramatic demand on Internet capacity. In response, internet service providers are exploring new data pricing approaches as economic countermeasures. However, previous pricing schemes are inadequate to provide tussle-resistance property that enables confidential price propagation and accurate bandwidth accounting. In this letter, we propose tussle-resistant Internet pricing mechanism (TRIP), which is built upon border gateway protocol and involves multiple cryptographic algorithms for price encryption and dissemination. TRIP effectively accomplishes source authentication and price confirmation, and leverages network capability to achieve bandwidth allocation and accounting. We confirm the efficiency of TRIP via comprehensive experiments.
Anthropometric Profile and Its Influence on the Vital Signs of Baja California College Students

An anthropometric study applied to 1,115 students of the Faculty of Chemical Sciences and Engineering of the Autonomous University of California. Thirteen individual measurements were taken in a sitting position. The results obtained allow forming a reliable anthropometric database for statistical studies and analysis and inferences of specific distributions, so the opinion of experts in occupational medicine recommendations may emit to reduce risks resulting in an alteration of the vital signs during the execution of their school activities. Another use of these analyses is to use them as a reliable reference for future deeper research, to the design of spaces, tools, utensils, workstations, with anthropometric dimensions and ergonomic characteristics suitable to use. Keywords—Anthropometry, vital signs, students.
Designing small wind turbines for highly turbulent sites

The use of small grid-connected wind turbines in the built environment is increasing. The international wind turbine design standard is based on open terrain sites, but in the built environment, the turbulence intensity is much higher than in open terrain and can lead to premature fatigue of turbines This paper compares the turbulence power spectral densities from direct measurement on the rooftop of Bunning Group Ltd’s warehouse at Port Kennedy, Western Australia, with predictions from the von Karman and Kaimal spectra used by turbulence models in the design standard. Both model spectra under estimate the magnitude of the measured values for all wind components although the Kaimal spectra provides more realistic values in terms of predicting the turbulence power spectra of lateral and vertical wind components in the built-environment. A corrected Kaimal model is proposed that has good agreement with measured values and can be viewed as a first step towards upgrading the existing standard with a dedicated design model for the built environment.
Comprehensive Detection and Discrimination of Campylobacter Species by Use of Confocal Micro-Raman Spectroscopy and Multilocus Sequence Typing

ABSTRACT A novel strategy for the rapid detection and identification of traditional and emerging Campylobacter strains based upon Raman spectroscopy (532 nm) is presented here. A total of 200 reference strains and clinical isolates of 11 different Campylobacter species recovered from infected animals and humans from China and North America were used to establish a global Raman spectroscopy-based dendrogram model for Campylobacter identification to the species level and cross validated for its feasibility to predict Campylobacter-associated food-borne outbreaks. Bayesian probability coupled with Monte Carlo estimation was employed to validate the established Raman classification model on the basis of the selected principal components, mainly protein secondary structures, on the Campylobacter cell membrane. This Raman spectroscopy-based typing technique correlates well with multilocus sequence typing and has an average recognition rate of 97.21%. Discriminatory power for the Raman classification model had a Simpson index of diversity of 0.968. Intra- and interlaboratory reproducibility with different instrumentation yielded differentiation index values of 4.79 to 6.03 for wave numbers between 1,800 and 650 cm−1 and demonstrated the feasibility of using this spectroscopic method at different laboratories. Our Raman spectroscopy-based partial least-squares regression model could precisely discriminate and quantify the actual concentration of a specific Campylobacter strain in a bacterial mixture (regression coefficient, >0.98; residual prediction deviation, >7.88). A standard protocol for sample preparation, spectral collection, model validation, and data analyses was established for the Raman spectroscopic technique. Raman spectroscopy may have advantages over traditional genotyping methods for bacterial epidemiology, such as detection speed and accuracy of identification to the species level.
A Low-Loss Compact 60-GHz Phase Shifter in 65-nm CMOS

This paper presents a 60-GHz low-loss compact 4-b phase shifter in a 65-nm CMOS. It is based on a 1-b high-pass/low-pass structure and a 3-b switched-filter structure, and employs fully custom-designed capacitors with a high quality factor for low insertion loss. The phase shifter with custom-designed capacitors reduces an insertion loss by 2.6 dB at 60 GHz. The average insertion loss is 8.1 dB at 60 GHz, and the return loss is better than 10.6 dB over a range of 57–66 GHz. The measured 16-output state of the fabricated phase shifter has a phase resolution of 22.5° with an rms phase error less than 5.5° over the 57–66 GHz range. The fabricated phase shifter has a compact core size of 0.42 mm <inline-formula> <tex-math notation="LaTeX">$\times0.22$ </tex-math></inline-formula> mm. To the best of our knowledge, this phase shifter achieves the lowest insertion loss and the smallest core area of all the published 60-GHz 360° -coverage passive CMOS phase shifters.
EFFECT OF TEMPERATURE AND GRAZING ON GROWTH AND REPRODUCTION OF FLOATING MACROCYSTIS SPP. (PHAEOPHYCEAE) ALONG A LATITUDINAL GRADIENT 1

Macroalgal rafts frequently occur floating in coastal waters of temperate regions of the world’s oceans. These rafts are considered important dispersal vehicles for associated organisms with direct development. However, environmental factors may limit the floating potential of kelp and thereby the dispersal of associated organisms. To examine the effect of water temperature and grazing on growth, reproductive output, and survival of floating Macrocystis spp. , experiments were conducted in outdoor tanks during austral summer 2006/2007 at three sites along the Chilean Pacific coast (20° S, 30° S, 40° S). At each site, Macrocystis spp. was maintained individually at three different water temperatures (ambient, ambient − 4°C, ambient + 4°C) and in the presence or absence of the amphipod grazer Peramphithoe femorata for 14 d. High water temperatures (>20°C) provoked rapid degradation of Macrocystis spp. rafts. At moderate temperatures (15°C–20°C), algal survival depended on the presence of associated grazers. In the absence of grazers, algal rafts gained in biomass while grazing caused considerable losses of algal biomass. Algal survival was the highest under cooler conditions (<15°C), where raft degradation was slow and grazer‐induced biomass losses were compensated by continuing algal growth. Our results indicate that floating kelp rafts can survive for long time periods at the sea surface, but survival depends on the interaction between temperature and grazing. We suggest that these processes limiting the survival of kelp rafts in warmer temperatures may act as a dispersal barrier for kelp and its associated passengers.