Miracle-dz/UniFAR-FTUs huggingface dataset:
Hyper‐processive and slower DNA chain elongation catalysed by DNA polymerase III holoenzyme purified from the dnaE173 mutator mutant of Escherichia coli

Background: A strong mutator mutation, dnaE173, leads to a Glu612 → Lys amino acid change in the α subunit of Escherichia coli DNA polymerase III (PolIII) holoenzyme and abolishes the proofreading function of the replicative enzyme without affecting the 3′ → 5′ exonuclease activity of the ɛ subunit. The dnaE173 mutator is unique in its ability to induce sequence‐substitution mutations, suggesting that an unknown function of the α subunit is hampered by the dnaE173 mutation.
Building a Knowledge Base of Morphosyntactic Terminology

This paper describes the beginning of an effort within the Linguist List’s Electronic Metastructure for Endangered Languages Data (E-MELD) project to develop markup recommendations for representing the morphosyntactic structures of the world’s endangered languages. Rather than proposing specific markup recommendations as in the Text Encoding Initiative (TEI), we propose to construct an environment for comparing data sets using possibly different markup schemes. The central feature of our proposed environment is an ontology of morphosyntactic terms with multiple inheritance and a variety of relations holding among the terms. We are developing our ontology using the Protege editor, and are extending an existing upper-level ontology known as
A Novel Preprocessing Method for Hectography Prints Based on Independent Component Analysis

Archives and cultural facilities consists of vast spectra of different document classes, many of which are not encountered today anymore. The digitization therefore calls for image enhancement and preprocessing solutions so far not required and hence unsolved. A prominent document class in this context is hectography, which was an inexpensive printing and duplication method, widely used throughout the 20th century. The major challenge with hectography is poor contrast on the one side and multiple degradation effects on the other side. In this paper a novel preprocessing method for hectography duplicates is proposed which leads to better Optical Character Recognition (OCR) results compared to traditional methods that operate on grayscale images. The proposed method is based on a linear mixing model used in independent component analysis. The problem of unwanted Gaussian noise components is considered as well.
Free to Choose: An Experimental Investigation of the Value of Free Choice

This study is the first economic experiment that tests the economic significance of the theory of psychological reactance (Brehm, 1966). For this purpose, I design an economic experiment in which subjects are asked to express their valuation of two-choice situations. In one case, subjects are given absolute freedom, whereas in another, the extent of their freedom of choice is limited. As the experimental data revealed, subjects’ valuation of free and limited choice situations did not differ significantly. Thus, in the experiment, the subjects did not display signs of reactance. In the end, the potential reasons of why the subjects did not exhibit reactance are discussed. The lessons derived from this study may serve as a future guide for testing the economic significance of the reactance theory.
CLEARPOND: Cross-Linguistic Easy-Access Resource for Phonological and Orthographic Neighborhood Densities

Past research has demonstrated cross-linguistic, cross-modal, and task-dependent differences in neighborhood density effects, indicating a need to control for neighborhood variables when developing and interpreting research on language processing. The goals of the present paper are two-fold: (1) to introduce CLEARPOND (Cross-Linguistic Easy-Access Resource for Phonological and Orthographic Neighborhood Densities), a centralized database of phonological and orthographic neighborhood information, both within and between languages, for five commonly-studied languages: Dutch, English, French, German, and Spanish; and (2) to show how CLEARPOND can be used to compare general properties of phonological and orthographic neighborhoods across languages. CLEARPOND allows researchers to input a word or list of words and obtain phonological and orthographic neighbors, neighborhood densities, mean neighborhood frequencies, word lengths by number of phonemes and graphemes, and spoken-word frequencies. Neighbors can be defined by substitution, deletion, and/or addition, and the database can be queried separately along each metric or summed across all three. Neighborhood values can be obtained both within and across languages, and outputs can optionally be restricted to neighbors of higher frequency. To enable researchers to more quickly and easily develop stimuli, CLEARPOND can also be searched by features, generating lists of words that meet precise criteria, such as a specific range of neighborhood sizes, lexical frequencies, and/or word lengths. CLEARPOND is freely-available to researchers and the public as a searchable, online database and for download at http://clearpond.northwestern. edu.
Trichodysplasia spinulosa-Associated Polyomavirus (TSV) and Merkel Cell Polyomavirus: Correlation between Humoral and Cellular Immunity Stronger with TSV

Merkel Cell Polyomavirus (MCV) is a common infectious agent likely to be involved in the pathogenesis of most Merkel cell carcinomas (MCC). Trichodysplasia spinulosa-associated polyomavirus (TSV), which exhibit high seroprevalence in general population, has been detected in trichodysplasia spinulosa (TS) skin lesions suggesting an etiological role for this disease. Previous studies have shown strong MCV-specific T-cell responses, while no data exist on T-cell immunity against TSV. In order to characterize Th-cell immunity against TSV, and to allow comparisons with the MCV-specific Th-cell immunity, we studied TSV-specific proliferation, IFN-γ, IL-10 and IL-13, and MCV-specific IFN-γ and IL-10 responses in 51 healthy volunteers, and in one MCC patient. Recombinant TSV and MCV VP1 virus-like particles (VLPs) were used as antigens. A significant correlation was found between virus-specific Th-cell and antibody responses with TSV; with MCV it proved weaker. Despite significant homology in amino acid sequences, Th-cell crossreactivity was not evident between these viruses. Some subjects seronegative to both TSV and MCV exhibited Th-cell responses to both viruses. The agent initially priming these Th-cells remains an enigma. As CD8+ cells specific to MCV T-Ag oncoprotein clearly provide an important defense against established MCC, the MCV VP1-specific Th-cells may, by suppressing MCV replication with antiviral cytokines such as IFN-γ, significantly contribute to preventing the full process of oncogenesis.
Accounting for Bias in the Evaluation of Creative Computational Systems: An Assessment of DARCI

Recent investigations into the assessment and evaluation of “creative” systems in the field of computational creativity have disclosed several problems common to research within the field. We perform a practical evaluation of the latest iteration of the creative system, DARCI, attempting to address some of these problems using a specially designed, but generalizable, online human survey. Of note, we address the complications of evaluator bias that are present in all assessments of creativity. Using our evaluation, we show that within its narrow domain, DARCI is able to produce artifacts that are rated at least as favorably as human counter parts across five aspects of creativity. Further, these artifacts tend to be more surprising and perceived as more difficult to produce than those created by human artists.
Influence of age on rectal tone and sensitivity to distension in healthy subjects

Hypersensitivity to rectal distension is frequently observed in patients with irritable bowel syndrome (IBS). However, few data are available about the influence of age on rectal sensory thresholds and tone. The aim of this study was to measure rectal sensory thresholds and tone with a barostat in 12 healthy subjects (aged 86 ± 4 years, eight females, four males) as compared with 12 young healthy male controls (26 ± 1 years). Isobaric phasic distensions were performed in the fasted state (increment of 4 mmHg, steps of 5 min, interval of 5 min). Rectal tone changes were then measured as changes in volume of the barostat bag, the pressure being kept constant. After a baseline recording of 1 h, a 1000‐kcal meal was served and the tone recorded until return to baseline.
Exploit-based Analysis of Attack Models

Protecting network-accessible resources from unauthorized use requires understanding of network vulnerability. Building attack models as chains of vulnerability exploits by an attacker can help locate flaws to prevent attacks. This paper presents an approach to automatically analyzing security attack models called exploit-based analysis. By using knowledge about exploitability of network vulnerabilities combined with a Markov computational process commonly used in link analysis, exploit based analysis ranks nodes in the attack model in order of their likelihoods of being compromised. The paper discusses the details of the approach, illustrates its use, and compares results with an existing technique.
p73 G4C14 to A4T14 polymorphism is associated with colorectal cancer risk and survival.

AIM To analyze the association between the p73 G4C14-to-A4T14 polymorphism (a.k.a., the GC/AT variation) and colorectal cancer risk and survival in the Korean population, and to evaluate the relationships between p73 polymorphism and the p73 protein expression or clinicopathological characteristics of colorectal cancer. METHODS Three hundred and eighty-three histologically confirmed cases and 469 healthy controls, recruited at one teaching hospital in Pusan, Korea from 2001 and 2007, were genotyped for p73 G4C14-to-A4T14 by PCR with confronting two-pair primers (PCR-CTPP) and the expression profile of p73 in cancer tissues (n = 383) was analyzed by immunohistochemistry. RESULTS Odds ratios (ORs) and 95% confidence intervals (CIs) were calculated by unconditional logistic regression model adjusted for age and gender. Compared with the GC/GC genotypes, the GC/AT and AT/AT genotypes were significantly associated with colorectal cancer risk (GC/AT vs GC/GC: OR = 1.46, 95% CI: 1.10-1.94; AT/AT vs GC/GC: 1.72, 0.98-3.03; P(trend) = 0.01). When stratified by age and gender, the association was restricted to those less than 60 years of age (GC/AT or AT/AT vs GC/GC: 2.22, 1.39-3.55) and male (GC/AT or AT/AT vs GC/GC: 1.91, 1.31-2.77). The expression of p73 was associated with invasion depth (P = 0.003) and advanced Duke's stage (P = 0.06) of colorectal cancer. The patients with the GC/GC genotype were associated with worse survival compared with those with the other genotypes (P = 0.02). However, no significant relationship was observed between the p73 G4C14-to-A4T14 polymorphism and p73 protein expression in cancer tissues. CONCLUSION Our results suggest that the p73 GC/AT polymorphism is associated with an increased colorectal cancer risk and survival in the Korean population.
Strong bending of the DNA double helix

During the past decade, the issue of strong bending of the double helix has attracted a lot of attention. Here, we overview the major experimental and theoretical developments in the field sorting out reliably established facts from speculations and unsubstantiated claims. Theoretical analysis shows that sharp bends or kinks have to facilitate strong bending of the double helix. It remains to be determined what is the critical curvature of DNA that prompts the appearance of the kinks. Different experimental and computational approaches to the problem are analyzed. We conclude that there is no reliable evidence that any anomalous behavior of the double helix happens when DNA fragments in the range of 100 bp are circularized without torsional stress. The anomaly starts at the fragment length of about 70 bp when sharp bends or kinks emerge in essentially every molecule. Experimental data and theoretical analysis suggest that kinks may represent openings of isolated base pairs, which had been experimentally detected in linear DNA molecules. The calculation suggests that although the probability of these openings in unstressed DNA is close to 10−5, it increases sharply in small DNA circles reaching 1 open bp per circle of 70 bp.
Scalable laws for stable network congestion control

Discusses flow control in networks, in which sources control their rates based on feedback signals received from the network links, a feature present in current TCP protocols. We develop a congestion control system which is arbitrarily scalable, in the sense that its stability is maintained for arbitrary network topologies and arbitrary amounts of delay. Such a system can be implemented in a decentralized way with information currently available in networks plus a small amount of additional signaling.
The Genealogy of Self-similar Fragmentations with Negative Index as a Continuum Random Tree

We encode a certain class of stochastic fragmentation processes, namely self-similar fragmentation processes with a negative index of self-similarity, into a metric family tree which belongs to the family of Continuum Random Trees of Aldous. When the splitting times of the fragmentation are dense near 0, the tree can in turn be encoded into a continuous height function, just as the Brownian Continuum Random Tree is encoded in a normalized Brownian excursion. Under mild hypotheses, we then compute the Hausdorff dimensions of these trees, and the maximal Holder exponents of the height functions.
Cultures in Community Question Answering

CQA services are collaborative platforms where users ask and answer questions. We investigate the influence of national culture on people's online questioning and answering behavior. For this, we analyzed a sample of 200 thousand users in Yahoo Answers from 67 countries. We measure empirically a set of cultural metrics defined in Geert Hofstede's cultural dimensions and Robert Levine's Pace of Life and show that behavioral cultural differences exist in community question answering platforms. We find that national cultures differ in Yahoo Answers along a number of dimensions such as temporal predictability of activities, contribution-related behavioral patterns, privacy concerns, and power inequality.
Oral steroid prophylaxis is effective in preventing esophageal strictures after large endoscopic resection

Background Strictures are frequent complications of large endoscopic mucosal resections (EMR) and endoscopic submucosal dissections of the esophagus. Local or systemic steroid therapy has shown promise in the prevention of secondary stenosis. The aim of this study was to evaluate the safety and efficacy of systemic steroid therapy following endoscopic resection of at least hemi-circumferential esophageal mucosa. Methods This was a single-center retrospective study in a tertiary center. We evaluated patients who were treated with oral steroids between July 2013 and September 2015, after undergoing a large EMR for Barrett’s esophagus associated with dysplasia or carcinoma. The steroid protocol used was an initial dose of 30 mg prednisolone, tapered over 8 weeks. Exclusion criteria were a previous attempt at radiofrequency ablation or resection. Results Thirty-one patients (27 men) were analyzed: 13 with low-grade dysplasia Barrett’s esophagus, 16 with in situ adenocarcinoma, 1 with pT1SM1 adenocarcinoma, and 1 with pT1SM2 adenocarcinoma. Twenty-eight resections (28/31) were completed (R0) in 1-3 sessions (median 2), while 3 resections were R1. The median length of Barrett’s esophagus was C3M5 (range C0M2-C10M11) according to the Prague classification. The median follow up was 10 months (range 4-17), during which 4 patients (13%) developed a secondary stenosis. All stenoses were successfully treated by endoscopic dilation (range 1-4). No complications related to dilation or to the steroid therapy were observed. Conclusions Our rate of secondary stricture was lower than expected, given the rates of 17-88% in published studies. Systemic oral steroid therapy seems to be effective in reducing potential esophageal stenosis after EMR. Complementary randomized studies are required to confirm whether systemic steroids are an effective primary prophylaxis for esophageal stenosis.
Screening Acute HIV Infections among Chinese Men Who Have Sex with Men from Voluntary Counseling & Testing Centers

Background Recent studies have shown the public health importance of identifying acute HIV infection (AHI) in the men who have sex with men (MSM) of China, which has a much higher risk of HIV transmission. However, cost-utility analyses to guide policy around AHI screening are lacking. Methodology/Principal Findings An open prospective cohort was recruited among MSM living in Liaoning Province, Northeast China. Blood samples and epidemiological information were collected every 10 weeks. Third-generation ELISA and rapid test were used for HIV antibody screening, western blot assay (WB) served for assay validation. Antibody negative specimens were tested with 24 mini-pool nucleic acid amplification testing (NAAT). Specimens with positive ELISA but negative or indeterminate WB results were tested with NAAT individually without mixing. A cost-utility analysis of NAAT screening was assessed. Among the 5,344 follow-up visits of 1,765 MSM in 22 months, HIV antibody tests detected 114 HIV chronic infections, 24 seroconverters and 21 antibody indeterminate cases. 29 acute HIV infections were detected with NAAT from 21 antibody indeterminate and 1,606 antibody negative cases. The HIV-1 prevalence and incidence density were 6.6% (95% CI: 5.5–7.9) and 7.1 (95% CI: 5.4–9.2)/100 person-years, respectively. With pooled NAAT and individual NAAT strategy, the cost of an HIV transmission averted was $1,480. The addition of NAAT after HIV antibody tests had a cost-utility ratio of $3,366 per gained quality-adjusted life year (QALY). The input-output ratio of NAAT was about 1∶16.9. Conclusions/Significance The HIV infections among MSM continue to rise at alarming rates. Despite the rising cost, adding pooled NAAT to the HIV antibody screening significantly increases the identification of acute HIV infections in MSM. Early treatment and target-oriented publicity and education programs can be strengthened to decrease the risk of HIV transmission and to save medical resources in the long run.
Estimation of blood velocity vectors using transverse ultrasound beam focusing and cross-correlation

Modern ultrasound scanners estimate the blood velocity by tracking the movement of the blood scatterers along the ultrasound beam. This is done by emitting pulsed ultrasound fields and finding the shift in position from pulse to pulse by correlating the received signals. Only the velocity component along the beam direction is found, and this is a serious limitation in the current scanners, since most blood vessels are parallel to the skin surface. A method to find the velocity across the vessel has been suggested by Bonnefous (1988). Here a number of parallel receive beams are measured and used in a correlation estimator to find the velocity across the beam. This approach is extended in this paper by making beamforming along the direction of the flow. A fairly broad beam is emitted and the received signal is then focused along a selected direction. This direction can be along the ultrasound beam or across it or in any direction to the beam. The focused lines, thus, follow the flow and a cross-correlation of lines from different pulses can find the movement of the blood particles between pulse emissions and, thus, the blood velocity. The new approach is investigated using the Field II simulation program. Simulations are shown for a parabolic velocity profile for flow-to-beam angles of 30, 45, 60, and 90 degrees using a 64 elements linear array with a center frequency of 3 MHz, a pitch of 0.3 mm, and an element height of 5 mm. The peak velocity in the parabolic flow was 0.5 m/s, and the pulse repetition frequency was 3.5 kHz. Using four pulse-echo lines, the parabolic flow profile was found with a standard deviation of 0.028 m/s at 60 degrees and 0.092 m/s at 90 degrees (transverse to the ultrasound beam), corresponding to accuracies of 5.6% and 18.4%. Using ten lines gave standard deviations of 0.021 m/s and 0.089 m/s, respectively, corresponding to accuracies of 4.2% and 17.8%.
Representing and reasoning over a taxonomy of part-whole relations

Many types of part-whole relations have been proposed in the literature to aid the conceptual modeller to choose the most appropriate type, but many of those relations lack a formal specification to give clear and unambiguous semantics to them. To remedy this, a formal taxonomy of types of mereological and meronymic part-whole relations is presented that distinguishes between transitive and intransitive relations and the kind of entity types that are related. The demand to use it effectively brings afore new requirements for automated reasoning over a hierarchy of relations. To ensure logically and ontologically correct inferencing over both the class and role hierarchy, the new reasoning service RBox compatibility for Description Logics reasoners is introduced. The proposed combination of formal semantics and the new reasoning service will improve the representation of the application domain when using part-whole relations in conceptual models and ontologies.
Religiosity gap reversed: how religious counsellors’ belief system presents when working with clients in a non-religious environment

ABSTRACT Most studies exploring the religiosity gap are concerned with non-religious counsellors and religious clients. Approaching this phenomenon from a reversed perspective, this study explores how counsellors’ religiosity presents when working with clients in a predominantly non-religious environment. Semi-structured interviews with 11 Czech counsellors who self-identify as Roman Catholic were subjected to thematic analysis. The analysis revealed seven main themes, divided into two main thematic domains: counsellors’ inner attitude towards the counselling process and direct interaction with clients. The findings are discussed in relation to the concept of religiosity gap, as well as training, supervision, and multicultural competencies of counsellors.
Double inverted pendulum decoupling control by adaptive terminal sliding-mode recurrent fuzzy neural network

An adaptive terminal sliding-mode recurrent fuzzy neural network ATSRFNN control system is developed to control a coupled double inverted pendulum system. The proposed ATSRFNN control system is composed of a recurrent fuzzy neural network RFNN controller and an adaptive terminal sliding ATS controller. The RFNN controller is designed to mimic an ideal controller, and the ATS controller is designed to cope with the approximation error and external disturbance. The simulation results show the proposed ATSRFNN control system can achieve better control performance and robustness in comparison with a hierarchical fuzzy sliding-mode control system.