Miracle-dz/UniFAR-FTUs huggingface dataset:
Defining the roles of individual residues in the single-stranded DNA binding site of PcrA helicase

Crystal structures and biochemical analyses of PcrA helicase provide evidence for a model for processive DNA unwinding that involves coupling of single-stranded DNA (ssDNA) tracking to a duplex destabilization activity. The DNA tracking model invokes ATP-dependent flipping of bases between several pockets on the enzyme formed by conserved aromatic amino acid residues. We have used site-directed mutagenesis to confirm the requirement of all of these residues for helicase activity. We also demonstrate that the duplex unwinding defects correlate with an inability of certain mutant proteins to translocate effectively on ssDNA. Moreover, the results define an essential triad of residues within the ssDNA binding site that comprise the ATP-driven DNA motor itself.
Logic-Based Query Optimization for Object Databases

We present a technique for transferring query optimization techniques, developed for relational databases, into object databases. We demonstrate this technique for ODMG database schemas defined in ODL and object queries expressed in OQL. The object schema is represented using a logical representation (Datalog). Semantic knowledge about the object data model, e.g., class hierarchy information, relationship between objects, etc., as well as semantic knowledge about a particular schema and application domain are expressed as integrity constraints. An OQL object query is represented as a logic query and query optimization is performed in the Datalog representation. We obtain equivalent (optimized) logic queries, and subsequently obtain equivalent (optimized) OQL queries for each equivalent logic query. We present one optimization technique for semantic query optimization (SQO) based on the residue technique of U. Charavarthy et al. (1990; 1986; 1988). We show that our technique generalizes previous research on SQO for object databases. We handle a large class of OQL queries, including queries with constructors and methods. We demonstrate how SQO can be used to eliminate queries which contain contradictions and simplify queries, e.g., by eliminating joins, or by reducing the access scope for evaluating a query to some specific subclass(es). We also demonstrate how the definition of a method or integrity constraints describing the method, can be used in optimizing a query with a method.
Therapists' Emotional Reactions to Patients as a Mediator in Cognitive Behavioural Treatment of Panic Disorder with Agoraphobia

The aims of this study were to examine whether therapists' emotional reactions to their patients mediate the effect of personality disorders and interpersonal problem behaviours on the outcome of treatment, focusing on an Axis I disorder; and whether therapists' reactions mediate the effect of personality disorders on the course of interpersonal problems. Therapists completed a checklist of emotional reactions to individual patients after the end of residential cognitive or guided mastery therapy for 46 inpatients with panic disorder with agoraphobia. The severity of DSM‐III‐R personality disorder was related to therapists' insecurity feelings, but not to interest and anger. A higher level of therapists' insecurity feelings was related to less reduction in self‐reported agoraphobic avoidance during treatment, whereas therapists' emotions were unrelated to symptomatic course after treatment. Therapists' insecurity feelings appeared partly to mediate the relationship between patients' severity of personality disorder and persistence of patients' interpersonal dominance and nurturance problems.
Regional outcomes of heart failure in Canada.

BACKGROUND Heart failure is a condition associated with significant mortality and morbidity. However, demographic features and outcomes following hospitalization for heart failure, and associated regional comparisons have not been performed in Canada. METHODS Anonymously rendered records of patients hospitalized for incident heart failure in Canada were selected from the Canadian Institute for Health Information discharge abstract and hospital morbidity databases from fiscal years 1997/1998 to 1999/2000. The demographics, in-hospital mortality rate and heart failure readmission rates were compared among provinces and health regions. RESULTS A total of 83,406 patients were hospitalized for heart failure across Canada during the study period. The number of cases increased dramatically with each decade after age 50 years, with 85% of hospitalized patients being age 65 years and over. On average, in-hospital mortality per index admission in Canada was 9.5 deaths per 100 hospitalized cases. While the greatest burden of readmissions was among those 65 years of age and over, heart failure readmission rates were similar across age groups. Among all patients surviving the index admission, heart failure readmission rates were 8.7%, 14.1% and 23.6% at 30 days, 90 days and one year, respectively. The highest age- and sex-adjusted in-hospital mortality rates were 11.9% (95% CI 10.6 to 13.2) in Newfoundland/Labrador and 11.6% (95% CI 10.6 to 12.7) in Nova Scotia. The highest readmission rates at one year were 26.9% (95% CI 24.9 to 28.9) in Newfoundland/Labrador, 26.3% (95% CI 25.0 to 27.7) in Saskatchewan and 25.2% (95% CI 24.3 to 26.1) in British Columbia. There were significant regional variations in heart failure readmission rates and mortality. CONCLUSIONS There is a great burden of heart failure in Canada, increasing significantly with age. The mortality and readmission rates for this condition are high and exhibit variation among health regions and provinces. Factors contributing to regional variations in these outcomes merit further study.
Focused ion beam fabrication of solidified ferritin into nanoscale volumes for compositional analysis using atom probe tomography

The purpose of this investigation was to conduct atom probe tomography (APT) analyses on ferritin specimens prepared with focused ion beam (FIB) to assess whether this approach can be used to effectively characterize biomaterials. Soft matter is particularly sensitive to ion beam exposure which can induce physical and chemical changes. We employ protective metal films and low‐energy ion fluence to mitigate potential problems that may be introduced by FIB. This study had two major objectives: (1) to qualitatively assess the viability of the specimens when subjected to the unique physical conditions of APT analysis, namely ultrahigh vacuum, high electric field, and thermal pulsing using a laser and (2) to quantitatively assess the data from such specimens under various experimental parameters and compare the results with appropriate control specimens. For the first objective, a range of experimental parameters were determined that met the basic criteria necessary to validate that ferritin‐based specimens prepared with FIB can retain structural integrity during APT analysis. Initial field evaporation time‐of‐flight mass spectrometry (TOF‐MS) data show that the specimens fabricated with FIB are capable of emitting ions under various laser pulsing conditions with a high electric field applied. For the second objective, the experimental parameter space was narrowed to a range that yielded data quality sufficient to produce meaningful comparison between the ferritin‐based specimens and the salt‐only controls.
A National Study of Nurse Leadership and Supports for Quality Improvement in Rural Hospitals

This study assessed the perceptions and actions of rural hospital nurse executives with regard to patient safety and quality improvement (QI). A national sample of rural hospital nurse executives (n = 300) completed a survey measuring 4 domains related to patient safety and QI: (a) patient “Safety Culture,” (b) adequacy of QI “Resources,” (c) “Barriers” related to QI, and (d) “Nurse Leader Engagement” in activities supporting QI. Perceptions of Safety Culture were strong but 47% of the Resources needed to carry out QI were inadequate, 29% of Barriers were moderate to major, and 25% of Nurse Leader Engagement activities were performed infrequently. Nurse Leader Engagement in quality-related activities was less frequent among nurses in isolated and small rural town hospitals compared with large rural city hospitals. To further QI, rural nurse executives may need to use their communications and actions to raise the visibility of QI.
Using Stated Preferences Data to Analyze Preferences for Full and Partial Retirement

Structural models explaining retirement decisions of individuals or households in an inter-temporal setting are typically hard to estimate using data on actual retirement decisions, because choice sets are complicated and uncertain and for a large part unobserved by the researcher. This paper describes an experiment in which both perceived retirement opportunities and preferences for retirement are measured. For the latter, respondents evaluate how attractive they find a number of hypothetical, simplified, retirement trajectories involving early retirement, late retirement, and gradual retirement, each with its own corresponding income path. The questions were fielded in the Dutch CentERpanel. The answers are used to estimate a stylized structural life-cycle model of retirement preferences. The results suggest that, for example, many respondents could be convinced to work part-time after age 65 before retiring completely at age 70 for a reasonable financial compensation. Simulations combining the information on perceived opportunities with estimated preferences also illustrate the importance of employer imposed restrictions on retirement and the scope for increasing labor force participation of the elderly by creating opportunities for gradual retirement.
High-Affinity Manganese Uptake by the Metal Transporter NRAMP1 Is Essential for Arabidopsis Growth in Low Manganese Conditions[C][W]

This study shows that, in order to acquire manganese when concentrations in the soil are limited, Arabidopsis relies on a root high-affinity manganese uptake system catalyzed by the metal transporter NRAMP1. The finding that overexpression of NRAMP1 produces large plants with increased manganese content paves the way for the biotechnological engineering of plants with improved biomass production. In contrast with many other essential metals, the mechanisms of Mn acquisition in higher eukaryotes are seldom studied and poorly understood. We show here that Arabidopsis thaliana relies on a high-affinity uptake system to acquire Mn from the soil in conditions of low Mn availability and that this activity is catalyzed by the divalent metal transporter NRAMP1 (for Natural Resistance Associated Macrophage Protein 1). The nramp1-1 loss-of-function mutant grows poorly, contains less Mn than the wild type, and fails to take up Mn in conditions of Mn limitation, thus demonstrating that NRAMP1 is the major high-affinity Mn transporter in Arabidopsis. Based on confocal microscopy observation of an NRAMP1-green fluorescent protein fusion, we established that NRAMP1 is localized to the plasma membrane. Consistent with its function in Mn acquisition from the soil, NRAMP1 expression is restricted to the root and stimulated by Mn deficiency. Finally, we show that NRAMP1 restores the capacity of the iron-regulated transporter1 mutant to take up iron and cobalt, indicating that NRAMP1 has a broad selectivity in vivo. The role of transporters of the NRAMP family is well established in higher eukaryotes for iron but has been controversial for Mn. This study demonstrates that NRAMP1 is a physiological manganese transporter in Arabidopsis.
Incremental outlier detection in data streams using local correlation integral

In this paper, an incremental outlier detection technique capable of dealing with a large amount of data is presented and evaluated in the context of intrusion detection. The proposed method is based on the LOcal Correlation Integral (LOCI for short). The detection technique consists of two parts. The first part named insertion receives the sequence of input point and updates Multi-granularity DEviation Factor (MDEF) of the point at intervals. The second part named deletion deletes one or a batch of points. This technique is able to process streaming data in a single scan. Moreover, the number of updates in the incremental LOCI algorithm per insertion/deletion of a single data record does not depend on the total number of data records. Experimental results with real life data sets show that the technique is capable of dealing with data streams, successfully detecting outlier.
Multicenter external validation of the ABCD2 score in triaging TIA patients

Objectives: A simple clinical score (ABCD2 score) has been introduced to triage TIA patients with a high early risk of stroke. External validation studies have yielded inconsistent results regarding the predictive ability of the ABCD2 score. We aimed to prospectively validate the former score in a multicenter case series study. Methods: We prospectively calculated the ABCD2 score (age [≥60 years: 1 point]; blood pressure [systolic >140 mm Hg or diastolic >90 mm Hg: 1[; clinical features [unilateral weakness: 2, speech disturbance without weakness: 1, other symptom: 0]; duration of symptoms [ <10 minutes: 0, 10–59 minutes: 1, ≥60 minutes: 2]; diabetes mellitus [yes: 1]) in consecutive TIA patients hospitalized in 3 tertiary care neurology departments across 2 different racial populations (white and Asian). Results: The 7-day and 90-day risks of stroke in the present case series (n = 148) were 8% (95% CI 4%–12%) and 16% (95% CI 10%–22%). The ABCD2 score accurately discriminated between TIA patients with high 7-day (c statistic 0.72, 95% CI 0.57–0.88) and 90-day (c statistic 0.75, 95% CI 0.65–0.86) risks of stroke. The 90-day risk of stroke was 7-fold higher in patients with an ABCD2 score >3 points (28%, 95% CI 18%–38%) than in patients with an ABCD2 score ≤3 points (4%, 95% CI 0%–9%). After adjustment for stroke risk factors, race, history of previous TIA, medication use before the index TIA and secondary prevention treatment strategies, an ABCD2 score of >2 was associated with a nearly 5-fold greater 90-day risk of stroke (hazard ratio 4.65, 95% CI 1.04–20.84, p = 0.045). Conclusion: Our findings externally validate the usefulness of the ABCD2 score in triaging TIA patients with a high risk of early stroke in a multiethnic sample of hospitalized patients. The present data support current guidelines endorsing the immediate hospitalization of patients with an ABCD2 score >2.
Phenotype of neoplastic cells in angioimmunoblastic T-cell lymphoma is consistent with activated follicular B helper T cells.

We read the letter by Grogg et al,[1][1] recently published in Blood, with great interest. The authors demonstrated that CD10+ T cells in angioimmunoblastic T-cell lymphoma[2][2] (AITL) coexpress CXCL13 and proposed that AITL is a neoplasm of germinal center (GC) T-helper cells. We have
Heterologous amplification of homologous beta-adrenoceptor desensitization in airway smooth muscle

the results provide no explanation for the observed adverse effects of racemic β 2 -adrenoceptor agonists in asthma. In single cell measurements R-salbutamol preferentially inhibits the contractile agonist-induced Ca 2+ -plateau by decreasing the amplitude of the Ca 2+ -oscillations. In addition, there is a differential susceptibility to β -agonist-induced inhibition of the Ca 2+ -transient and - plateau, depending both on the cellular condition (attached vs non-attached) and on the contractile agonist used
European Nautical Tourists: Exploring Destination Image Perceptions

Purpose – Nautical tourism is considered to be an under-exploited research area, if we take into account its evolution and growth prospects. This lack of knowledge is probably one of the main reasons the sector has not reached its maximum. The present paper aims at exploring the European nautical tourists´ perceptions of image, in relation to the type of nautical sport they carry out and the type of nautical destination they visit. Methodology – The research was conducted in the Canary Islands and Morocco during 2013 and 2014. The sample covered 433 European nautical tourists pursuing different nautical sports and was organised into two groups. Structured questionnaires with personal interviews were implemented. Choosing a mature nautical destination and an emerging one enriched the comparative approach for the study. The findings indicate there are clearly similar profiles amongst the groups of tourists visiting both regions, and that the perceived image varies between a nautical tourist doing sailing and a nautical tourist motivated by other nautical sports. The data analysis reveals that perceptions also vary according to the more intensive and extensive use of the destinations. Originality – This empirical study provides useful insights into the demand for nautical tourism, the perceptions and evaluations of the ports and marinas as well as the destinations themselves, which can be used as a guide for the tourism industry managers and the Government Authorities to develop more effective marketing and positioning strategies. The study of the destination image in nautical tourism is a contribution to the progress beyond the state of the sector.
Water savings potentials of irrigation systems:: global simulation of processes and linkages

Global agricultural production is heavily sustained by irrigation, but irrigation system efficiencies are often surprisingly low. However, our knowledge of irrigation efficiencies is mostly confined to rough indicative estimates for countries or regions that do not account for spatiotemporal heterogeneity due to climate and other biophysical dependencies. To allow for refined estimates of global agricultural water use, and of water saving and water productivity potentials constrained by biophysical processes and also non-trivial downstream effects, we incorporated a process-based representation of the three major irrigation systems (surface, sprinkler, and drip) into a bio- and agrosphere model, LPJmL. Based on this enhanced model we provide a gridded world map of irrigation efficiencies that are calculated in direct linkage to differences in system types, crop types, climatic and hydrologic conditions, and overall crop management. We find pronounced regional patterns in beneficial irrigation efficiency (a refined irrigation efficiency indicator accounting for crop-productive water consumption only), due to differences in these features, with the lowest values ( 60 %) in Europe and North America. We arrive at an estimate of global irrigation water withdrawal of 2469 km 3 (2004–2009 average); irrigation water consumption is calculated to be 1257 km 3 , of which 608 km 3 are non-beneficially consumed, i.e., lost through evaporation, interception, and conveyance. Replacing surface systems by sprinkler or drip systems could, on average across the world's river basins, reduce the non-beneficial consumption at river basin level by 54 and 76 %, respectively, while maintaining the current level of crop yields. Accordingly, crop water productivity would increase by 9 and 15 %, respectively, and by much more in specific regions such as in the Indus basin. This study significantly advances the global quantification of irrigation systems while providing a framework for assessing potential future transitions in these systems. In this paper, presented opportunities associated with irrigation improvements are significant and suggest that they should be considered an important means on the way to sustainable food security.
Concurrent Log-Structured Memory for Many-Core Key-Value Stores

Key-value stores are an important tool in managing and accessing large in-memory data sets. As many applications benefit from having as much of their working state fit into main memory, an important design of the memory management of modern key-value stores is the use of log-structured approaches, enabling efficient use of the memory capacity, by compacting objects to avoid fragmented states.However, with the emergence of thousand-core and peta-byte memory platforms (DRAM or future storage-class memories) log-structured designs struggle to scale, preventing parallel applications from exploiting the full capabilities of the hardware: careful coordination is required for background activities (compacting and organizing memory) to remain asynchronous with respect to the use of the interface, and for insertion operations to avoid contending for centralized resources such as the log head and memory pools.In this work, we present the design of a log-structured key-value store called Nibble that incorporates a multi-head log for supporting concurrent writes, a novel distributed epoch mechanism for scalable memory reclamation, and an optimistic concurrency index. We implement Nibble in the Rust language in ca. 4000 lines of code, and evaluate it across a variety of data-serving workloads on a 240-core cache-coherent server. Our measurements show Nibble scales linearly in uniform YCSB workloads, matching competitive non-log-structured key-value stores for write- dominated traces at 50 million operations per second on 1 TiB-sized working sets. Our memory analysis shows Nibble is efficient, requiring less than 10% additional capacity, whereas memory use by non-log-structured key-value store designs may be as high as 2x.
Retrospective analysis of whole genome sequencing compared to prospective typing data in further informing the epidemiological investigation of an outbreak of Shigella sonnei in the UK

SUMMARY The aim of this study was to retrospectively assess the value of whole genome sequencing (WGS) compared to conventional typing methods in the investigation and control of an outbreak of Shigella sonnei in the Orthodox Jewish (OJ) community in the UK. The genome sequence analysis showed that the strains implicated in the outbreak formed three phylogenetically distinct clusters. One cluster represented cases associated with recent exposure to a single strain, whereas the other two clusters represented related but distinct strains of S. sonnei circulating in the OJ community across the UK. The WGS data challenged the conclusions drawn during the initial outbreak investigation and allowed cases of dysentery to be implicated or ruled out of the outbreak that were previously misclassified. This study showed that the resolution achieved using WGS would have clearly defined the outbreak, thus facilitating the promotion of infection control measures within local schools and the dissemination of a stronger public health message to the community.
Reconfigurable Narrow-Frame Antenna for Heptaband WWAN/LTE Smartphone Applications

A compact frequency-reconfigurable narrow-frame antenna for heptaband smartphone applications is presented. The width of the no-ground portion to support the antenna is quite narrow of only 5 mm, which meets the requirements of the popular narrow-frame smartphone designs with larger touchscreens. Moreover, the reconfigurable technology is employed to achieve wide bandwidth coverage with a small volume. By combining two working states, the GSM850/900/1800/1900/UMTS2100/LTE2300/2500 operation is achieved. Detailed considerations of the design are studied in this letter, and the proposed antenna is successfully simulated, fabricated, and measured.
Assessing Texture Descriptors for Seismic Image Retrieval

Much work has been done on the assessment of texture descriptors for image retrieval in many domains. In this work, we evaluate the accuracy and performance of three wellknown texture descriptors – Gabor Filters, GLCM, and LBP – for seismic image retrieval. These subsurface images pose challenges yet not thoroughly investigated in previous works, which are addressed and evaluated in our experiments. We asked for domain experts to annotate two seismic cubes, Penobscot 3D and Netherlands F3, and used them to evaluate texture descriptors, corresponding parameters, and similarity metrics with the potential to retrieve visually similar regions of the considered datasets. While GLCM is used in the vast majority of works in this area, our findings indicate that LBP has the potential to produce satisfying results with lower computational cost.