Miracle-dz/UniFAR-FTUs huggingface dataset:
Characterization of the helper proteins for the assembly of tail fibers of coliphages T4 and lambda

Assembly of tail fibers of coliphage T4 requires the action of helper proteins. In the absence of one of these, protein 38 (p38), p37, constituting the distal part of the long tail fiber, fails to oligomerize. In the absence of the other, p57, p34 (another component of the long tail fiber), p37, and p12 (the subunit of the short tail fiber) remain unassembled. p38 can be replaced by the Tfa (tail fiber assembly) protein (pTfa) of phage lambda, which has the advantage of remaining soluble even when produced in massive amounts. The mechanisms of action of the helpers are unknown. As a first step towards elucidation of these mechanisms, p57 and pTfa have been purified to homogeneity and have been crystallized. The identity of gene 57 (g57), not known with certainty previously, has been established. The 79-residue protein p57 represents a very exotic polypeptide. It is oligomeric and acidic (an excess of nine negative charges). It does not contain Phe, Trp, Tyr, His, Pro, and Cys. Only 25 N-terminal residues were still able to complement a g57 amber mutant, although with a reduced efficiency. In cells overproducing the protein, it assumed a quasi-crystalline structure in the form of highly ordered fibers. They traversed the cells longitudinally (and thus blocked cell division) with a diameter approaching that of the cell and with a hexagonal appearance. The 194-residue pTfa is also acidic (an excess of 13 negative charges) and is likely to be dimeric.
Reasons for attrition from a smoking cessation program.

The present study examined various psychosocial variables that may influence success in a stop smoking program (QuitSmart) used by the North Texas Veterans Health Care Service (NTVHCS). The QuitSmart program utilizes the Stages of Change Model, with its focus on the last three stages (preparation, action, and maintenance). It was proposed that factors including shame-proneness, guilt, anger/hostility, depression, self-efficacy - both global and smoking situational, neuroticism, and level of nicotine dependence might individually or in combination predict attrition from the NTVHCS smoking cessation program. Results indicate that shame-proneness, guilt, anger/hostility, and depression did not individually predict attrition. Persons with high levels of smoking situational self-efficacy tend to utilize self-change strategies leading to greater success in smoking cessation. Participants with a psychological diagnosis, when combined with neuroticism and shame-proneness, appear to have more difficulty with cessation than those with only a medical diagnosis. Clinical implications and suggestions for change to the NTVHCS smoking cessation program are discussed.
Autism Spectrum Disorders in Africa : Current Challenges in Identification , Assessment , and Treatment : A Report on the International Child Neurology Association Meeting on ASD in Af

Prevalence of autism spectrum disorders has increased over recent years, however, little is known about the identification and management of autism spectrum disorder in Africa. This report summarizes a workshop on autism spectrum disorder in Africa under the auspices of the International Child Neurology Association and the African Child Neurology Association through guided presentations and working group reports, focusing on identification, diagnosis, management, and community support. A total of 47 delegates participated from 14 African countries. Although there was a huge variability in services across the countries represented, numbers of specialists assessing and managing autism spectrum disorder was small relative to populations served. Strategies were proposed to improve identification, diagnosis, management and support delivery for individuals with autism spectrum disorder across Africa in these culturally diverse, low-resource settings. Emphasis on raising public awareness through community engagement and improving access to information and training in autism spectrum disorder. Special considerations for the cultural, linguistic, and socioeconomic factors within Africa are discussed.
User Adaptive Restoration for Incorrectly-Segmented Utterances in Spoken Dialogue Systems

Ideally, the users of spoken dialogue systems should be able to speak at their own tempo. The systems thus need to correctly interpret utterances from various users, even when these utterances contain disfluency. In response to this issue, we propose an approach based on a posteriori restoration for incorrectly segmented utterances. A crucial part of this approach is to classify whether restoration is required or not. We improve the accuracy by adapting the classifier to each user. We focus on the dialogue tempo of each user, which can be obtained during dialogues, and determine the correlation between each user’s tempo and the appropriate thresholds for the classification. A linear regression function used to convert the tempos into thresholds is also derived. Experimental results showed that the proposed user adaptation for two classifiers, thresholding and decision tree, improved the classification accuracies by 3.0% and 7.4%, respectively, in ten-fold cross validation.
Relation of executive functioning to pragmatic outcome following severe traumatic brain injury.

PURPOSE This study was designed to explore the behavioral nature of pragmatic impairment following severe traumatic brain injury (TBI) and to evaluate the contribution of executive skills to the experience of pragmatic difficulties after TBI. METHOD Participants were grouped into 43 TBI dyads (TBI adults and close relatives) and 43 control dyads. All TBI participants had sustained severe injury (mean posttraumatic amnesia duration = 45.19 days, SD = 39.15) due to a moving vehicle-related trauma. A minimum of 2 years had elapsed since injury (M = 5.36 years, SD = 3.61). The La Trobe Communication Questionnaire (LCQ; Douglas, O'Flaherty, & Snow, 2000) was administered to all participants. Measures of executive function included the following: the FAS verbal fluency task (Spreen & Benton, 1969), the Speed and Capacity of Language Processing test (Baddeley, Emslie, & Nimmo-Smith, 1992), and the Rey Auditory Verbal Learning Task (Rey, 1964). RESULTS Perceptions of TBI participants and their relatives were significantly correlated (r = .63, p < .001) and significantly different from those of controls, F(1, 84) = 37.2, p < . 001. Pragmatic difficulties represented violations in 3 domains of Grice's (1975) Cooperative Principle (Quantity, Relation, and Manner), and executive function measures predicted 37% (32% adjusted) of the variability in LCQ scores. CONCLUSIONS The study demonstrates evidence of a significant association between executive impairment and the pragmatic communication difficulties experienced by individuals with TBI.
Trial by Fire: Teleoperated Robot Targets Chernobyl

The blast that destroyed Unit 4 of the Chernobyl Nuclear Power Plant (CNPP) 12 years ago prompted a firestorm of scientific, technological, political, and economic proposals for managing the worst nuclear accident to date. Following a meeting of the G-7 nations-the United States, Canada, Britain, France, Italy, Germany, and Japan-and Ukrainian representatives, the US Department of Energy (DOE) and National Aeronautics and Space Administration (NASA) organized and funded a "dream team" of experts in robotics as well as computer hardware and software for the "Pioneer Project". Pioneer is a specialized, tethered, bulldozer-like robot equipped with stereo vision for real-time 3D mapping, a core-drilling and sampling apparatus, and an array of radiation and other sensor tools for remotely investigating Unit 4. The team has scheduled Pioneer's deployment at Chernobyl for November 1998.
Gene Expression Analysis Using a High‐Resolution DNA Microarray of Peripheral Whole Blood Immediately Before and After Leukocytapheresis for Rheumatoid Arthritis

Leukocytapheresis (LCAP) is a safe, unique therapy pertaining to intractable rheumatoid arthritis (RA) even in cases of drug allergy or infectious states. To investigate how to represent LCAP efficacy, we have conducted gene expression analyses from the peripheral blood of RA patients treated with non‐woven polyethylene terephthalate filters. Peripheral blood samples were collected immediately before and after treatment from eight RA patients who received LCAP. Among these patients, all of them achieved 20% improvement in the core set of the American College of Rheumatology (ACR20), and thus, they were confirmed as LCAP responders. Gene expression analysis was done with a high‐resolution DNA microarray. The results of each of the two groups' gene expression values (immediately before and after LCAP) were calculated using Welch's t‐test. Calculations were performed with a statistical software R.basic package: if the P‐value was less than 0.05, this was seen as a significant change. In a comparison of 25 370 gene expressions, the number of genes showing a P‐value < 0.05 in the upregulating group was 2110, and in the downregulating group it was 1864. The results of pathway analysis using the MetaCore program indicate that gene groups work for cytoskeletal remodeling are upregulated, and genes related to immune responses, such as antigens presenting via major histocompatibility complex class I and II, are downregulated just after LCAP. These findings may relate to LCAP efficacy for RA patients, but this needs further investigation.
Word Order Change in Icelandic: From OV to VO

While Modern Icelandic exhibits a virtually uniform VO order in the VP, Old(er) Icelandic had both VO order and OV order, as well as ‘mixed’ word order patterns. In this volume, the author both examines the various VP-word order patterns from a descriptive and statistical point of view and provides a synchronic and diachronic analysis of VP-syntax in Old(er) Icelandic in terms of generative grammar. Her account makes use of a number of independently motivated ideas, notably remnant-movement of various kinds of predicative phrase, and the long movement associated with “restructuring” phenomena, to provide an analysis of OV orders and, correspondingly, a proposal as to which aspect of Icelandic syntax must have changed when VO word order became the norm: the essential change is loss of VP-extraction from VP. Although this idea is mainly supported here for Icelandic, it has numerous implications for the synchronic and diachronic analysis of other Germanic languages.
Red-black tree architecture for P2P media streaming

With the recent surge of Internet enabled portable devices, such as smart phones and tablets, it has resulted in a much faster growth of the global Internet usage. Most of the usage is due to the use of social media platforms where streaming media is used heavily. Most of the researches conducted were to address the issues related to overall delivered quality in a resource-constraint streaming environment as well as the issues related to the scalability of the overall media streaming system. While there are other areas of research that have seen significant work in addressing the limitations posed by the current network infrastructure, devices capabilities and also on the characteristics of the streaming media themselves. These research projects address different factors that lead to alleviating network capacity bottlenecks. The success of Peer-to-Peer (P2P) file sharing systems inspired the development of P2P streaming systems for delivering online multimedia service in the last few years. P2P networks are broadly categorized into two main network architecture; a tree-based architecture and a mesh-based architecture. Despite the advantages offered by tree-based streaming architecture, it is lacking in maintaining a balanced tree architecture which is needed to ensure a consistent quality of service. In this paper, we investigate and evaluate our proposed red-black tree-based streaming architecture as compared to a traditional tree-based architecture for media streaming performance. The simulations were conducted under various real-world scenarios and evaluated using different critical performance metrics that affect the overall streaming quality and performance.
Kernel Robust Bias-Aware Prediction under Covariate Shift

Under covariate shift, training (source) data and testing (target) data differ in input space distribution, but share the same conditional label distribution. This poses a challenging machine learning task. Robust Bias-Aware (RBA) prediction provides the conditional label distribution that is robust to the worstcase logarithmic loss for the target distribution while matching feature expectation constraints from the source distribution. However, employing RBA with insufficient feature constraints may result in high certainty predictions for much of the source data, while leaving too much uncertainty for target data predictions. To overcome this issue, we extend the representer theorem to the RBA setting, enabling minimization of regularized expected target risk by a reweighted kernel expectation under the source distribution. By applying kernel methods, we establish consistency guarantees and demonstrate better performance of the RBA classifier than competing methods on synthetically biased UCI datasets as well as datasets that have natural covariate shift.
A survey of poliomyelitis virus antibodies in French Morocco.

Summary A serological survey of antibodies to all three types of poliomyelitis virus has been carried out in an urban and semiurban population in French Morocco. The rates at which neutralizing antibodies and complement-fixing antibodies have been acquired by this population according to different age groups are herein reported. Heavy infection and a rapid development of antibodies at an early age characterize the pattern obtained. The results indicate the presence of actively acquired neutralizing antibodies, and presumably immunity, to all three types of poliomyelitis virus in about 80 per cent of the population by the time children have reached 5 years of age. The percentages persist in all older age groups. Complement-fixing antibodies, on the other hand, are present largely in the juvenile population, and fall to low levels in those over 10 years of age. Since the complement fixing antibody in poliomyelitis is a transient one, this suggests that active infection is occurring only in young children in the Moroccan population. As a control disease, presumably spread by human association, mumps was selected, and antibody patterns to mumps virus were determined. Results indicate that mumps infection also comes early to this population but in so far as a comparison is warranted, apparently not as early as does poliomyelitis virus infection. The findings differ sharply from those which might be expected from a United States city studied at about the same latitude. Their interpretation has some bearing on the relationship between antibody and immunity in the infant, pointing to a close relationship between the two. The results also point to the fact that living conditions in this population are apparently particularly conducive to the spread of infantile infections with both poliomyelitis and mumps but particularly the former.
A Low-Voltage, Low-Power, and Low-Noise UWB Mixer Using Bulk-Injection and Switched Biasing Techniques

This paper presents a low-voltage, low-power, low-noise, and ultra-wideband (UWB) mixer using bulk-injection and switched biasing techniques. The bulk-injection technique is implemented for a low supply voltage, thus resulting in low power consumption. This technique also allows for a flat conversion gain over a wide range of frequencies covering the full UWB band; this is a result of the integration of the RF transconductance stage and the local oscillator switching stage into a single transistor that is able to eliminate parasitic effects. Moreover, since the bulk-injection transistors of the mixer are designed to operate in the subthreshold region, current dissipation is reduced. A switched biasing technique for the tail current source, in place of static biasing, is adopted to reduce noise. The effects of modulated input signals, such as AM and FM, are simulated and measured to demonstrate the robustness of the switched biasing technique. The proposed mixer offers a measured conversion gain from 7.6 to 9.9 dB, a noise figure from 11.7 to 13.9 dB, and input third-order intercept point from - 10 to - 15.5 dBm, over 2.4 to 11.9 GHz, while consuming only 0.88 mW from a 0.8-V supply voltage. The chip size including the test pads is 0.62×0.58 mm2 using a 0.18-μm RF CMOS process.
Phasing for medical sequencing using rare variants and large haplotype reference panels

Motivation: There is growing recognition that estimating haplotypes from high coverage sequencing of single samples in clinical settings is an important problem. At the same time very large datasets consisting of tens and hundreds of thousands of high-coverage sequenced samples will soon be available. We describe a method that takes advantage of these huge human genetic variation resources and rare variant sharing patterns to estimate haplotypes on single sequenced samples. Sharing rare variants between two individuals is more likely to arise from a recent common ancestor and, hence, also more likely to indicate similar shared haplotypes over a substantial flanking region of sequence. Results: Our method exploits this idea to select a small set of highly informative copying states within a Hidden Markov Model (HMM) phasing algorithm. Using rare variants in this way allows us to avoid iterative MCMC methods to infer haplotypes. Compared to other approaches that do not explicitly use rare variants we obtain significant gains in phasing accuracy, less variation over phasing runs and improvements in speed. For example, using a reference panel of 7420 haplotypes from the UK10K project, we are able to reduce switch error rates by up to 50% when phasing samples sequenced at high-coverage. In addition, a single step rephasing of the UK10K panel, using rare variant information, has a downstream impact on phasing performance. These results represent a proof of concept that rare variant sharing patterns can be utilized to phase large high-coverage sequencing studies such as the 100 000 Genomes Project dataset. Availability and implementation: A webserver that includes an implementation of this new method and allows phasing of high-coverage clinical samples is available at https://phasingserver.stats.ox.ac.uk/. Contact: marchini@stats.ox.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online.
Serre functors for Lie algebras and superalgebras

We propose a new realization, using Harish-Chandra bimodules, of the Serre functor for the BGG category $\mathcal{O}$ associated to a semi-simple complex finite dimensional Lie algebra. We further show that our realization carries over to classical Lie superalgebras in many cases. Along the way we prove that category $\mathcal{O}$ and its parabolic generalizations for classical Lie superalgebras are categories with full projective functors. As an application we prove that in many cases the endomorphism algebra of the basic projective-injective module in (parabolic) category $\mathcal{O}$ for classical Lie superalgebras is symmetric. As a special case we obtain that in these cases the algebras describing blocks of the category of finite dimensional modules are symmetric. We also compute the latter algebras for the superalgebra $\mathfrak{q}(2)$.
Early development of rostrum saw-teeth in a fossil ray tests classical theories of the evolution of vertebrate dentitions

In classical theory, teeth of vertebrate dentitions evolved from co-option of external skin denticles into the oral cavity. This hypothesis predicts that ordered tooth arrangement and regulated replacement in the oral dentition were also derived from skin denticles. The fossil batoid ray Schizorhiza stromeri (Chondrichthyes; Cretaceous) provides a test of this theory. Schizorhiza preserves an extended cartilaginous rostrum with closely spaced, alternating saw-teeth, different from sawfish and sawsharks today. Multiple replacement teeth reveal unique new data from micro-CT scanning, showing how the ‘cone-in-cone’ series of ordered saw-teeth sets arrange themselves developmentally, to become enclosed by the roots of pre-existing saw-teeth. At the rostrum tip, newly developing saw-teeth are present, as mineralized crown tips within a vascular, cartilaginous furrow; these reorient via two 90° rotations then relocate laterally between previously formed roots. Saw-tooth replacement slows mid-rostrum where fewer saw-teeth are regenerated. These exceptional developmental data reveal regulated order for serial self-renewal, maintaining the saw edge with ever-increasing saw-tooth size. This mimics tooth replacement in chondrichthyans, but differs in the crown reorientation and their enclosure directly between roots of predecessor saw-teeth. Schizorhiza saw-tooth development is decoupled from the jaw teeth and their replacement, dependent on a dental lamina. This highly specialized rostral saw, derived from diversification of skin denticles, is distinct from the dentition and demonstrates the potential developmental plasticity of skin denticles.
Chronic bronchitis before age 50 years predicts incident airflow limitation and mortality risk

Background: Previous studies on the relationship of chronic bronchitis to incident airflow limitation and all-cause mortality have provided conflicting results, with positive findings reported mainly by studies that included populations of young adults. This study sought to determine whether having chronic cough and sputum production in the absence of airflow limitation is associated with onset of airflow limitation, all-cause mortality and serum levels of C-reactive protein (CRP) and interleukin-8 (IL-8), and whether subjects’ age influences these relationships. Methods: 1412 participants in the long-term Tucson Epidemiological Study of Airway Obstructive Disease who at enrolment (1972–1973) were 21–80 years old and had FEV1/FVC (forced expiratory volume in 1 s/forced vital capacity) ⩾70% and no asthma were identified. Chronic bronchitis was defined as cough and phlegm production on most days for ⩾3 months in two or more consecutive years. Incidence of airflow limitation was defined as the first follow-up survey with FEV1/FVC <70%. Serum IL-8 and CRP levels were measured in cryopreserved samples from the enrolment survey. Results: After adjusting for covariates, chronic bronchitis at enrolment significantly increased the risk for incident airflow limitation and all-cause mortality among subjects <50 years old (HR 2.2, 95% CI 1.3 to 3.8; and HR 2.2, 95% CI 1.3 to 3.8; respectively), but not among subjects ⩾50 years old (HR 0.9, 95% CI 0.6 to 1.4; and HR 1.0, 95% CI 0.7 to 1.3). Chronic bronchitis was associated with increased IL-8 and CRP serum levels only among subjects <50 years old. Conclusions: Among adults <50 years old, chronic bronchitis unaccompanied by airflow limitation may represent an early marker of susceptibility to the effects of cigarette smoking on systemic inflammation and long-term risk for chronic obstructive pulmonary disease and all-cause mortality.