Miracle-dz/UniFAR-FTUs huggingface dataset:
P and S velocity structure of the crust and the upper mantle beneath central Java from local tomography inversion

Here we present the results of local source tomographic inversion beneath central Java. The data set was collected by a temporary seismic network. More than 100 stations were operated for almost half a year. About 13,000 P and S arrival times from 292 events were used to obtain three-dimensional (3-D) Vp, Vs, and Vp/Vs models of the crust and the mantle wedge beneath central Java. Source location and determination of the 3-D velocity models were performed simultaneously based on a new iterative tomographic algorithm, LOTOS-06. Final event locations clearly image the shape of the subduction zone beneath central Java. The dipping angle of the slab increases gradually from almost horizontal to about 70°. A double seismic zone is observed in the slab between 80 and 150 km depth. The most striking feature of the resulting P and S models is a pronounced low-velocity anomaly in the crust, just north of the volcanic arc (Merapi-Lawu anomaly (MLA)). An algorithm for estimation of the amplitude value, which is presented in the paper, shows that the difference between the fore arc and MLA velocities at a depth of 10 km reaches 30% and 36% in P and S models, respectively. The value of the Vp/Vs ratio inside the MLA is more than 1.9. This shows a probable high content of fluids and partial melts within the crust. In the upper mantle we observe an inclined low-velocity anomaly which links the cluster of seismicity at 100 km depth with MLA. This anomaly might reflect ascending paths of fluids released from the slab. The reliability of all these patterns was tested thoroughly.
Knowledge about traumatic dental injuries in the permanent dentition: A survey of Lithuanian dentists

BACKGROUND/AIMS In Lithuania, dental trauma cases are often treated by general dentists, but it is unknown whether their age, self-evaluation of trauma knowledge and practice location can predict their actual knowledge and management of trauma cases. The aim of this study was to evaluate whether these factors can be used to predict the actual knowledge and management of trauma cases. METHODS A 2-part questionnaire included 17 multiple-choice questions about practitioners' demographics, their self-evaluated knowledge and how frequently they treated traumatized permanent teeth as well as 13 clinical scenarios reflecting a variety of clinical trauma cases and their complications. A total of 980 randomly selected general dentists, representing 5 Lithuanian counties, participated in the study. RESULTS The response rate was 59.4% (n = 582). Overall, 82.3% of general dentists reported that they treated only a few dental trauma cases and 14.4% chose to refer their patients; 55.1% of dentists considered their dental traumatology knowledge to be sufficient but incomplete and 34.0% self-evaluated their knowledge as insufficient. The most knowledge (based on self-evaluation) was reported by the younger dentists (≤50 years; P = .004). The mean correct knowledge score was 7.6 ± 2.2 of the 13 clinical scenarios. Both bivariate and multivariate analyses showed that greater trauma-related knowledge was associated with a younger age. Better knowledge was observed amongst the dentists who self-evaluated their own knowledge as sufficient or as comprehensive. CONCLUSION Lithuanian general dentists have insufficient dental traumatology knowledge. Better knowledge was observed amongst younger dentists (≤50 years).
Tracing carbon fixation in phytoplankton—compound specific and total 13C incorporation rates

Measurement of total primary production using 13C incorporation is a widely established tool. However, these bulk measurements lack information about the fate of fixed carbon: the production of major cellular compounds (carbohydrates, amino acids, fatty acids, and DNA/RNA) is affected by for instance nutrient availability as their C:N:P requirements differ. Here, we describe an approach to combine established methods in gas chromatography/isotope ratio mass spectrometry (GC/C‐IRMS) and recently developed methods in liquid chromatography/IRMS (LC/IRMS) to trace stable isotope incorporation into neutral carbohydrates, amino acids, and fatty acids, and compare their production to total carbon fixation rates. We conducted a trial study at stations in the North Sea where different nutrients were limiting. There was variation in the fate of fixed carbon at these sites. The majority of fixed carbon (64–71%) was incorporated into neutral carbohydrates, followed by amino acids (19–32%) and fatty acids (4–9%). The sum of carbon fixation into these three fractions accounted for 81–116% of total carbon fixation. P‐ and N‐limitation increased the biosynthesis of storage lipids and storage carbohydrates while N‐limitation decreased synthesis of amino acid proline with a concurrent increase in glutamic acid + glutamine. This new approach provides the capability to determine direct effects of resource limitation and the consequences for the physiological state of a phytoplankton community. It may thereby enable us to evaluate the overall quality of phytoplankton as a food source for higher trophic levels or trace consumption of phytoplankton through the food web.
Deterministic Truncation of Linear Matroids

Let M=(E,I) be a matroid of rank n. A k-truncation of M is a matroid M′=(E,I′) such that for any A⊆ E, A∈ ∈I′ if and only if |A|≤ k and A∈ I. Given a linear representation, A, of M, we consider the problem of finding a linear representation, Ak, of the k-truncation of M. A common way to compute Ak is to multiply the matrix A with a random k× n matrix, yielding a simple randomized algorithm. Thus, a natural question is whether we can compute Ak deterministically. In this article, we settle this question for matrices over any field in which the field operations can be done efficiently. This includes any finite field and the field of rational numbers (Q). Our algorithms are based on the properties of the classical Wronskian determinant, and the folded Wronskian determinant, which was recently introduced by Guruswami and Kopparty [23, 24] and Forbes and Shpilka [14]. Our main conceptual contribution in this article is to show that the Wronskian determinant can also be used to obtain a representation of the truncation of a linear matroid in deterministic polynomial time. An important application of our result is a deterministic algorithm to compute representative sets over linear matroids, which derandomizes a result of Fomin et al. [11, 12]. This result derandomizes several parameterized algorithms, including an algorithm for ℓ-Matroid Parity to which several problems, such as ℓ-Matroid Intersection, can be reduced.
Invading Mnemiopsis leidyi as a potential threat to Baltic fish.

The occurrence of the ctenophore Mnemiopsis leidyi as a new invasive species in the Baltic Sea and the potential consequences for fish stock recruitment was investigated in spring 2007. The study focused on the Bornholm Basin, which serves as the major spawning ground for cod and sprat, the commercially most important fish stocks in the Baltic. The distribution pattern of M. leidyi revealed a substantial overlap with cod eggs. The observed predation of M. leidyi on eggs has the potential to alter the recruitment success of cod, which is the top predator in the system and, thus, to change the Baltic food-web structure.
Newer antibiotics for the treatment of peritoneal dialysis-related peritonitis

Peritonitis is a debilitating infectious complication of peritoneal dialysis (PD). Drug-resistant bacterial peritonitis typically has a lower response rate to antibiotics. In the past 15 years, newer antibiotics with activities against drug-resistant Gram-positive bacteria have been developed. In most circumstances, peritonitis due to methicillin-resistant staphylococci responds to vancomycin. If vancomycin cannot be used due to allergy and/or non-susceptibility, there is increasing evidence that linezolid and daptomycin are the drugs of choice. It is reasonable to start linezolid orally or intravenously, but subsequent dose reduction may be necessary in case of myelosuppression. Daptomycin can be given intravenously or intraperitoneally and has excellent anti-biofilm activity. Other treatment options for drug-resistant Gram-positive bacterial peritonitis include teicoplanin, tigecycline and quinupristin/dalfopristin. Teicoplanin is not available in some countries (e.g. the USA). Tigecycline can only be given intravenously. Quinupristin/dalfopristin is ineffective against Enterococcus faecalis and there is only low-quality evidence to support its efficacy in the treatment of peritonitis. Effective newer antibiotics against drug-resistant Gram-negative bacteria are lacking. Polymyxins can be considered, but evidence on its efficacy is limited. In this review, we will discuss the potential use of newer antibiotics in the treatment of drug-resistant bacterial peritonitis in PD patients.
Indolent T‐lymphoblastic proliferation concomitant with acinic cell carcinoma mimicking T‐lymphoblastic lymphoma: case report and literature review

Indolent T‐lymphoblastic proliferation (iT‐LBP) is a non‐clonal benign condition showing extrathymic proliferation of T‐lymphoblasts positive for CD3, CD4, CD8, and TdT. Isolated iT‐LBP has been observed, but the majority of iT‐LBPs have been seen in conjunction with other disorders, including Castleman disease, hepatocellular carcinoma, follicular dendritic cell tumours, angioimmunoblastic T‐cell lymphoma, myasthenia gravis, and acinic cell carcinoma (ACC). The clinical course of iT‐LBP is indolent, and no therapy is usually required. A major concern is misdiagnosis as T‐lymphoblastic lymphoma, and a correct diagnosis of iT‐LBP often requires not only pathological analysis but also careful monitoring of the clinical course. The aim of this study was to broaden the knowledge of pathologists and physicians concerning this as yet not well‐recognised entity.
Patient outcomes of genetic counseling: Assessing the impact of different approaches to family history collection

No studies have yet evaluated whether different modalities for the collection of family history data influence patient outcomes of genetic counseling. We retrospectively compared outcomes of genetic counseling between patients whose family history (Fhx) was collected (1) via telephone prior to their appointment (FhxPrior) or (2) during the appointment (FhxDuring). We used a psychiatric genetic counseling clinic database, where information about demographics and Fhx timing is recorded, and patients complete the Genetic Counseling Outcomes Scale (GCOS, measuring empowerment) and Illness Management Self‐Efficacy Scale (IMSES) immediately prior to (T1) and 1 month after their appointment (T2). We used ANCOVA to evaluate the effect of the Fhx method on patient outcomes at T2. Complete data were available for 240 patients and were used for analysis (FhxPrior, n = 206; FhxDuring, n = 34). GCOS and IMSES scores increased from T1 to T2 (P < .0005 and P = .004, respectively). Although there was no difference between groups for GCOS (P = .412), T2 IMSES scores were significantly higher for FhxPrior than FhxDuring after controlling for T1 scores (P = .011). Our data suggest that obtaining Fhx via telephone prior to genetic counseling may lead to greater increases in patients’ self‐efficacy as compared to obtaining Fhx during the genetic counseling appointment.
Positive and negative affectivity, stress, and well-being in African-Americans: Initial demonstration of a polynomial regression and response surface methodology approach

Objective: The extent to which positive (PA) and negative (NA) affect conjointly impact well-being is not yet well understood. Additionally, research investigating the role of affectivity in maintaining well-being among ethnic and racial minorities is scant. The current research demonstrates how polynomial regression and response surface methodology (PR and RSM) may be used to better understand how PA and NA jointly influence stress and well-being. Design: In Study 1, 291 African-American undergraduates (Mage = 22.91, SD = 6.91; 67% female) completed measures of affectivity and psychological well-being. In Study 2, a community sample of 117 African-Americans (Mage = 31.87, SD = 13.83; 69% female) completed affectivity measures and a laboratory-based social stressor task to assess links between affectivity and salivary cortisol reactivity. Main outcome measures: Study 1 included life satisfaction, perceived stress and self-reported depressive symptoms. Study 2 included salivary cortisol reactivity. Results: Across both studies, PA ascendency (i.e. high PA combined with low NA) was associated with better well-being, while NA ascendancy (i.e. high NA combined with low PA) was associated with poorer outcomes. Conclusion: PR and RSM may provide new insight into the conjoint influence of PA and NA on health and well-being. We discuss potential implications for affectivity research, including race-related explorations.
Moonstruck Primates: Owl Monkeys (Aotus) Need Moonlight for Nocturnal Activity in Their Natural Environment

Primates show activity patterns ranging from nocturnality to diurnality, with a few species showing activity both during day and night. Among anthropoids (monkeys, apes and humans), nocturnality is only present in the Central and South American owl monkey genus Aotus. Unlike other tropical Aotus species, the Azara's owl monkeys (A. azarai) of the subtropics have switched their activity pattern from strict nocturnality to one that also includes regular diurnal activity. Harsher climate, food availability, and the lack of predators or diurnal competitors, have all been proposed as factors favoring evolutionary switches in primate activity patterns. However, the observational nature of most field studies has limited an understanding of the mechanisms responsible for this switch in activity patterns. The goal of our study was to evaluate the hypothesis that masking, namely the stimulatory and/or inhibitory/disinhibitory effects of environmental factors on synchronized circadian locomotor activity, is a key determinant of the unusual activity pattern of Azara's owl monkeys. We use continuous long-term (6–18 months) 5-min-binned activity records obtained with actimeter collars fitted to wild owl monkeys (n = 10 individuals) to show that this different pattern results from strong masking of activity by the inhibiting and enhancing effects of ambient luminance and temperature. Conclusive evidence for the direct masking effect of light is provided by data showing that locomotor activity was almost completely inhibited when moonlight was shadowed during three lunar eclipses. Temperature also negatively masked locomotor activity, and this masking was manifested even under optimal light conditions. Our results highlight the importance of the masking of circadian rhythmicity as a determinant of nocturnality in wild owl monkeys and suggest that the stimulatory effects of dim light in nocturnal primates may have been selected as an adaptive response to moonlight. Furthermore, our data indicate that changes in sensitivity to specific environmental stimuli may have been an essential key for evolutionary switches between diurnal and nocturnal habits in primates.
Functional and phylogenetic diversity determine woody productivity in a temperate forest

Abstract Understanding the relationships between biodiversity and ecosystem productivity has become a central issue in ecology and conservation biology studies, particularly when these relationships are connected with global climate change and species extinction. However, which facets of biodiversity (i.e. taxonomic, functional, and phylogenetic diversity) account most for variations in productivity are still not understood very well. This is especially true with regard to temperate forest ecosystems. In this study, we used a dataset from a stem‐mapped permanent forest plot in northeastern China exploring the relationships between biodiversity and productivity at different spatial scales (20 × 20 m; 40 × 40 m; and 60 × 60 m). The influence of specific environmental conditions (topographic conditions) and stand maturity (expressed by initial stand volume and biomass) were taken into account using the multivariate approach known as structural equation models. The variable “Biodiversity” includes taxonomic (Shannon), functional (FDis), and phylogenetic diversity (PD). Biodiversity–productivity relationships varied with the spatial scales. At the scale of 20 × 20 m, PD and FDis significantly affected forest biomass productivity, while Shannon had only indirect effects. At the 40 × 40 m and 60 × 60 m scales, biodiversity and productivity were weakly correlated. The initial stand volume and biomass were the most important drivers of forest productivity. The local environmental conditions significantly influenced the stand volume, biomass, biodiversity, and productivity. The results highlight the scale dependency of the relationships between forest biodiversity and productivity. The positive role of biodiversity in facilitating forest productivity was confirmed at the smaller scales. Our findings emphasize the fundamental role of environmental conditions in determining forest ecosystem performances. The results of this study provide a better understanding of the underlying ecological processes that influence specific forest biodiversity and productivity relationships.
Influenza Vaccination for Immunocompromised Patients: Systematic Review and Meta-Analysis from a Public Health Policy Perspective

Background Immunocompromised patients are vulnerable to severe or complicated influenza infection. Vaccination is widely recommended for this group. This systematic review and meta-analysis assesses influenza vaccination for immunocompromised patients in terms of preventing influenza-like illness and laboratory confirmed influenza, serological response and adverse events. Methodology/Principal Findings Electronic databases and grey literature were searched and records were screened against eligibility criteria. Data extraction and risk of bias assessments were performed in duplicate. Results were synthesised narratively and meta-analyses were conducted where feasible. Heterogeneity was assessed using I2 and publication bias was assessed using Begg's funnel plot and Egger's regression test. Many of the 209 eligible studies included an unclear or high risk of bias. Meta-analyses showed a significant effect of preventing influenza-like illness (odds ratio [OR] = 0.23; 95% confidence interval [CI] = 0.16–0.34; p<0.001) and laboratory confirmed influenza infection (OR = 0.15; 95% CI = 0.03–0.63; p = 0.01) through vaccinating immunocompromised patie nts compared to placebo or unvaccinated controls. We found no difference in the odds of influenza-like illness compared to vaccinated immunocompetent controls. The pooled odds of seroconversion were lower in vaccinated patients compared to immunocompetent controls for seasonal influenza A(H1N1), A(H3N2) and B. A similar trend was identified for seroprotection. Meta-analyses of seroconversion showed higher odds in vaccinated patients compared to placebo or unvaccinated controls, although this reached significance for influenza B only. Publication bias was not detected and narrative synthesis supported our findings. No consistent evidence of safety concerns was identified. Conclusions/Significance Infection prevention and control strategies should recommend vaccinating immunocompromised patients. Potential for bias and confounding and the presence of heterogeneity mean the evidence reviewed is generally weak, although the directions of effects are consistent. Areas for further research are identified.
Finite Element Model for Masonry

A method for the in-plane analysis of clay masonry walls is presented. The proposed finite element model reproduces the nonlinear characteristics of masonry caused by material nonlinearity and progressivee joint failure. Masonry is considered as an assemblage of elastic brick continuum elements acting in conjunction with linkage elements simulating the mortar joints. The joint elements are assumed to have high compressive strength (with nonlinear deformation characteristics), low tensile strength, and limited shear strength depending upon the bond strength and degree of compression present. The material properties for this model are determined from uniaxial tests on bricks and masonry panels. Tests on a masonry deep beam are used as a basis for comparison between predicted theory and experimental evidence.
Evaluation of two autoinducer‐2 quantification methods for application in marine environments

This study evaluated two methods, namely high performance liquid chromatography with fluorescence detection (HPLC‐FLD) and Vibrio harveyi BB170 bioassay, for autoinducer‐2 (AI‐2) quantification in marine samples. Using both methods, the study also investigated the stability of AI‐2 in varying pH, temperature and media, as well as quantified the amount of AI‐2 signals in marine samples.
Viral DNA-Dependent Induction of Innate Immune Response to Hepatitis B Virus in Immortalized Mouse Hepatocytes

ABSTRACT Hepatitis B virus (HBV) infects hundreds of millions of people worldwide and causes acute and chronic hepatitis, cirrhosis, and hepatocellular carcinoma. HBV is an enveloped virus with a relaxed circular (RC) DNA genome. In the nuclei of infected human hepatocytes, conversion of RC DNA from the incoming virion or cytoplasmic mature nucleocapsid (NC) to the covalently closed circular (CCC) DNA, which serves as the template for producing all viral transcripts, is essential to establish and sustain viral replication. A prerequisite for CCC DNA formation is the uncoating (disassembly) of NCs to expose their RC DNA content for conversion to CCC DNA. We report here that in an immortalized mouse hepatocyte cell line, AML12HBV10, in which RC DNA exposure is enhanced, the exposed viral DNA could trigger an innate immune response that was able to modulate viral gene expression and replication. When viral gene expression and replication were low, the innate response initially stimulated these processes but subsequently acted to shut off viral gene expression and replication after they reached peak levels. Inhibition of viral DNA synthesis or cellular DNA sensing and innate immune signaling diminished the innate response. These results indicate that HBV DNA, when exposed in the host cell cytoplasm, can function to trigger an innate immune response that, in turn, modulates viral gene expression and replication. IMPORTANCE Chronic infection by hepatitis B virus (HBV) afflicts hundreds of millions worldwide and is sustained by the episomal covalently closed circular (CCC) DNA in the nuclei of infected hepatocytes. Release of viral genomic DNA from cytoplasmic nucleocapsids (NCs) (NC disassembly or uncoating) is a prerequisite for its conversion to CCC DNA, which can also potentially expose the viral DNA to host DNA sensors and trigger an innate immune response. We have found that in an immortalized mouse hepatocyte cell line in which efficient CCC DNA formation was associated with enhanced exposure of nucleocapsid-associated DNA, the exposed viral DNA indeed triggered host cytoplasmic DNA sensing and an innate immune response that was able to modulate HBV gene expression and replication. Thus, HBV can, under select conditions, be recognized by the host innate immune response through exposed viral DNA, which may be exploited therapeutically to clear viral persistence.