Miracle-dz/UniFAR-FTUs huggingface dataset:
Predicting survival of lung transplantation candidates with idiopathic interstitial pneumonia: does PaO(2) predict survival?

OBJECTIVE To find a parameter that would discriminate between the patients with idiopathic interstitial pneumonia who survived to undergo transplantation and those who died while waiting to undergo transplantation. METHODS A retrospective review was performed of all lung transplant referrals for idiopathic interstitial pneumonia that were listed with United Network for Organ Sharing at the University of California San Diego from January 1990 to February 1999. Of the 331 patients who were listed, 48 met the eligibility criteria. Patient demographics, radiographic studies, pathology reports, and the results of resting and exercise cardiopulmonary function tests were recorded from each patient's chart. Patients were divided into the following two groups: those patients who survived until transplantation and those still waiting were classified as "alive"; and those patients who died before undergoing transplantation were classified as "deceased. " RESULTS Forty-three of 48 patients had a pathologic diagnosis. The cohort included 25 patients with usual interstitial pneumonitis, 3 patients with nonspecific interstitial pneumonitis, 1 patient with desquamative interstitial pneumonitis, and 14 patients with interstitial lung disease of unknown etiology. The only significant difference between the two groups was resting PaO(2) (p = 0.035). A stepwise multivariate analysis demonstrated that PaO(2) and FEV(1)/FVC ratio were significantly associated with survival (hazards ratio, 1.06; confidence interval, 0.99 to 1.13; p = 0.019). CONCLUSIONS A survival analysis using PaO(2) and FEV(1)/FVC ratio values proved to be statistically significant, but a prospective trial is needed to determine the clinical relevance of these parameters for predicting survival in patients with idiopathic interstitial pneumonia.
Emergence of apospory and bypass of meiosis via apomixis after sexual hybridisation and polyploidisation

Hybridisation and polyploidy are major forces contributing to plant speciation. Homoploid (2x) and heteroploid (3x) hybrids, however, represent critical stages for evolution due to disturbed meiosis and reduced fertility. Apomixis – asexual reproduction via seeds – can overcome hybrid sterility, but requires several concerted alterations of developmental pathways to result in functional seed formation. Here, we analyse the reproductive behaviours of homo- and heteroploid synthetic hybrids from crosses between sexual diploid and tetraploid Ranunculus auricomus species to test the hypothesis that developmental asynchrony in hybrids triggers the shift to apomictic reproduction. Evaluation of male and female gametophyte development, viability and functionality of gametes shows developmental asynchrony, whereas seed set and germinability indicate reduced fitness in synthetic hybrids compared to sexual parents. We present the first experimental evidence for spontaneous apospory in most hybrids as an alternative pathway to meiosis, and the appearance of functional apomictic seeds in triploids. Bypassing meiosis permits these triploid genotypes to form viable seed and new polyploid progeny. Asynchronous development causes reduced sexual seed set and emergence of apospory in synthetic Ranunculus hybrids. Apomixis is functional in triploids and associated with drastic meiotic abnormalities. Selection acts to stabilise developmental patterns and to tolerate endosperm dosage balance shifts which facilitates successful seed set and establishment of apomictic lineages.
Translesion DNA synthesis-assisted non-homologous end-joining of complex double-strand breaks prevents loss of DNA sequences in mammalian cells

Double strand breaks (DSB) are severe DNA lesions, and if not properly repaired, may lead to cell death or cancer. While there is considerable data on the repair of simple DSB (sDSB) by non-homologous end-joining (NHEJ), little is known about the repair of complex DSBs (cDSB), namely breaks with a nearby modification, which precludes ligation without prior processing. To study the mechanism of cDSB repair we developed a plasmid-based shuttle assay for the repair of a defined site-specific cDSB in cultured mammalian cells. Using this assay we found that repair efficiency and accuracy of a cDSB with an abasic site in a 5′ overhang was reduced compared with a sDSB. Translesion DNA synthesis (TLS) across the abasic site located at the break prevented loss of DNA sequences, but was highly mutagenic also at the template base next to the abasic site. Similar to sDSB repair, cDSB repair was totally dependent on XrccIV, and altered in the absence of Ku80. In contrast, Artemis appears to be specifically involved in cDSB repair. These results may indicate that mammalian cells have a damage control strategy, whereby severe deletions are prevented at the expense of the less deleterious point mutations during NHEJ.
Extremality for Gallager’s Reliability Function  $E_{0}$

We describe certain extremalities for Gallager's E<sub>0</sub> function evaluated under the uniform input distribution over the class of binary input discrete memoryless channels; The results characterize the extremality of the E<sub>0</sub>(ρ) curves of the binary erasure channel and the binary symmetric channel among all the E<sub>0</sub>(ρ) curves that can be generated by the class of binary discrete memoryless channels whose E<sub>0</sub>(ρ) curves pass through a given point (ρ<sub>0</sub>, ε<sub>0</sub>), for some ρ<sub>0</sub> > -1.
Phase II trial of intratumoral administration of ONYX-015, a replication-selective adenovirus, in patients with refractory head and neck cancer.

PURPOSE To determine the safety, humoral immune response replication, and activity of multiple intratumoral injections of ONYX-015 (replication selective adenovirus) in patients with recurrent squamous cell carcinoma of the head and neck (SCCHN). PATIENTS AND METHODS This phase II trial enrolled patients with SCCHN who had recurrence/relapse after prior conventional treatment. Patients received ONYX-015 at a dose of 2 x 10(11) particles via intratumoral injection for either 5 consecutive days (standard) or twice daily for 2 consecutive weeks (hyperfractionated) during a 21-day cycle. Patients were monitored for tumor response, toxicity, and antibody formation. RESULTS Forty patients (30 standard and 10 hyperfractionated) received 533 injections of ONYX-015. Standard treatment resulted in 14% partial to complete regression, 41% stable disease, and 45% progressive disease rates. Hyperfractionated treatment resulted in 10% complete response, 62% stable disease, and 29% progressive disease rates. Treatment-related toxicity included mild to moderate fever (67% overall) and injection site pain (47% on the standard regimen, 80% on the hyperfractionated regimen). Detectable circulating ONYX-015 genome suggestive of intratumoral replication was identified in 41% of tested patients on days 5 and 6 of cycle 1; 9% of patients had evidence of viral replication 10 days after injection during cycle 1, and no patients had evidence of replication > or = 22 days after injection. CONCLUSION ONYX-015 can be safely administered via intratumoral injection to patients with recurrent/refractory SCCHN. ONYX-015 viremia is transient. Evidence of modest antitumoral activity is suggested.
Learning Outcomes of the Inquiry-in-Action Model for Chemistry Experimentation

There is overwhelming evidence supporting the decline of science education in Liberia. In an effort to contribute to the solution, we conducted a study to examine the impact of inquiry-based experimentation and conventional demonstration on the conceptual understanding of solutions and solubility among grade eleven students. We also investigated the relationship between students' achievement scores in solutions and solubility and their science inquiry process skills. A cluster random sample of eight schools was initially selected from 12 out of 31 high schools that had the necessary space and materials for experimentation. Using a Non-equivalent control group research design, the experimental group received instruction using inquiry-based experimentation, while the control group received instruction using traditional demonstration methods, for a period of six weeks. The results were analyzed using the Mann-Whitney U, and Wilcoxon Signed Rank tests. The findings indicated that inquiry-based experimentation reduced students' anxiety and increased their confidence in chemistry experiments. Although the inquiry-in-action model enhanced learners' conceptual understanding of solutions and solubility, it did not significantly improve their mastery of the mathematical components of the test. However, it did significantly enhance students' science inquiry process skills. It should be noted that while the inquiry-in-action model positively influenced learners' attitudes toward their preferences, behavior, and anxieties in chemistry experiments, it also led to a general demotivation to learn chemistry through experimentation. Additionally, there was a positive correlation between students' attitudes toward teaching and learning chemistry through experiments and their science inquiry process skills. However, this correlation was stronger between students' attitudes towards the demonstration of experiments and their science inquiry process skills compared to the attitudes towards the inquiry-in-action model and science inquiry process skills. This suggests that the traditional demonstration method is not entirely ineffective, and a combination of both demonstration and inquiry-based experimentation approaches may be a viable way to maximize the benefits of science experiments.
Specific non-monotonous interactions increase persistence of ecological networks

The relationship between stability and biodiversity has long been debated in ecology due to opposing empirical observations and theoretical predictions. Species interaction strength is often assumed to be monotonically related to population density, but the effects on stability of ecological networks of non-monotonous interactions that change signs have not been investigated previously. We demonstrate that for four kinds of non-monotonous interactions, shifting signs to negative or neutral interactions at high population density increases persistence (a measure of stability) of ecological networks, while for the other two kinds of non-monotonous interactions shifting signs to positive interactions at high population density decreases persistence of networks. Our results reveal a novel mechanism of network stabilization caused by specific non-monotonous interaction types through either increasing stable equilibrium points or reducing unstable equilibrium points (or both). These specific non-monotonous interactions may be important in maintaining stable and complex ecological networks, as well as other networks such as genes, neurons, the internet and human societies.
A Middle Triassic pachypleurosaur (Diapsida: Eosauropterygia) from a restricted carbonate ramp in the Western Carpathians (Gutenstein Formation, Fatric Unit): paleogeographic implications

Abstract An eosauropterygian skeleton found in the Middle Triassic (upper Anisian) Gutenstein Formation of the Fatric Unit (Demänovská dolina Valley, Low Tatra Mountains, Slovakia) represents the earliest known occurrence of marine tetrapods in the Western Carpathians. The specimen represents a partly articulated portion of the postcranial skeleton (nine dorsal vertebrae, coracoid, ribs, gastral ribs, pelvic girdle, femur and one zeugopodial element). It is assigned to the Pachypleurosauria, more precisely to the Serpianosaurus–Neusticosaurus clade based on the following combination of features: (1) small body size; (2) morphology of vertebrae, ribs and femur; (3) tripartite gastral ribs; and (4) microanatomy of the femur as revealed by μCT. Members of this clade were described from the epicontinental Germanic Basin and the Alpine Triassic (now southern Germany, Switzerland, Italy), and possibly from Spain. This finding shows that pachypleurosaur reptiles attained a broader geographical distribution during the Middle Triassic, with their geographical range reaching to the Central Western Carpathians. Pachypleurosaurs are often found in sediments formed in shallow, hypersaline carbonate-platform environments. The specimen found here occurs in a succession with vermicular limestones in a shallow subtidal zone and stromatolitic limestones in a peritidal zone, indicating that pachypleurosaurs inhabited hypersaline, restricted carbonate ramps in the Western Carpathians.
Reduction on OFF-responses of Electroretinogram in Monkeys with Long-term High Intraocular Pressure

Background: There are ON- and OFF-pathways in the normal vertebrate retina. Short- and long-flash electroretinogram (ERG) are suitable methods to observe the function of ON- and OFF-pathways in vivo, respectively. It is clear that high intraocular pressure (IOP) might cause dysfunction of cone-dominated photopic negative response (PhNR) in monkeys with high IOP in ON-pathway. However, whether cone-dominated OFF-responses are also affected is less known. The aim of this study was to observe photopic OFF-responses of ERG in monkeys with high IOP. Methods: Nine monkeys were involved in the experiment from January 2006 to December 2016. High IOP was induced in the right eye by laser coagulation of the mid-trabecular meshwork in five monkeys. Six years after the laser coagulation, both short- and long-flash of the photopic ERG were recorded. Stimulus light was red flashes superimposed on a blue background. Four normal monkeys were examined under the same ERG protocols as controls. Paired t-test was used to compare the difference of each ERG parameter between the lasered eye and the fellow eye. Analysis of variance (ANOVA) with Tukey adjustment was adopted to calculate the differences among the lasered eye, the fellow eye, and the eyes of normal monkeys. Results: The mean amplitude of a-wave (11.73 ± 2.05) and PhNR (8.67 ± 2.44) in lasered eyes was significantly lower than that of a-wave (21.47 ± 3.15) and PhNR (22.05 ± 3.42) in fellow eyes (P = 0.03 and P = 0.01, respectively) in response to short flash. The mean amplitude of d-wave (1.60 ± 0.59) and i-wave (3.13 ± 0.64) was significantly reduced in the lasered eyes than that of d-wave (4.01 ± 0.56) and i-wave (8.79 ± 1.75) in the fellow eyes (P = 0.02 and P = 0.02, respectively) in response to long flash. Conclusions: Reduced OFF-responses are recorded in monkeys with high IOP when dysfunction of photoreceptor is involved. The reduced OFF-responses to long-flash stimulus show evidence of anomalous retinal circuitry in glaucomatous retinopathy.
Flortaucipir F 18 Quantitation Using Parametric Estimation of Reference Signal Intensity

PET imaging of tau pathology in Alzheimer disease may benefit from the use of white matter reference regions. These regions have shown reduced variability compared with conventional cerebellar regions in amyloid imaging. However, they are susceptible to contamination from partial-volume blurring of tracer uptake in the cortex. We present a new technique, PERSI (Parametric Estimation of Reference Signal Intensity), for flortaucipir F 18 count normalization that leverages the advantages of white matter reference regions while mitigating potential partial-volume effects. Methods: Subjects with a clinical diagnosis of Alzheimer disease, mild cognitive impairment, or normal cognition underwent T1-weighted MRI and florbetapir imaging (to determine amyloid [Aβ] status) at screening and flortaucipir F 18 imaging at single or multiple time points. Flortaucipir F 18 images, acquired as 4 × 5 min frames 80 min after a 370-MBq injection, were motion-corrected, averaged, and transformed to Montreal Neurological Institute (MNI) space. The PERSI reference region was calculated for each scan by fitting a bimodal gaussian distribution to the voxel-intensity histogram within an atlas-based white matter region and using the center and width of the lower-intensity peak to identify the voxel intensities to be included. Four conventional reference regions were also evaluated: whole cerebellum, cerebellar gray matter, atlas-based white matter, and subject-specific white matter. SUVr (standardized uptake value ratio) was calculated for a statistically defined neocortical volume of interest. Performance was evaluated with respect to test–retest variability in a phase 2 study of 21 subjects (5–34 d between scans). Baseline variability in controls (SD of SUVr and ΔSUVr) and effect sizes for group differences (Cohen d; Aβ-positive impaired vs. Aβ-negative normal) were evaluated in another phase 2 study with cross-sectional data (n = 215) and longitudinal data (n = 142/215; 18 ± 2 mo between scans). Results: PERSI showed superior test–retest reproducibility (1.84%) and group separation ability (cross-sectional Cohen d = 9.45; longitudinal Cohen d = 2.34) compared with other reference regions. Baseline SUVr variability and ΔSUVr were minimal in Aβ control subjects with no specific flortaucipir F 18 uptake (SUVr, 1.0 ± 0.04; ΔSUVr, 0.0 ± 0.02). Conclusion: PERSI reduced variability while enhancing discrimination between diagnostic cohorts. Such improvements could lead to more accurate disease staging and robust measurements of changes in tau burden over time for the evaluation of putative therapies.
Enhancement of experimental actinomycosis in mice by Eikenella corrodens

The infectivity of Actinomyces israelii in a susceptible-weanling-mouse was increased by the presence of Eikenella corrodens in the inoculum. A minimal infecting dose of 1.7 X 10(7) CFU of A. israelii was required to establish chronic lesions after an intraperitoneal injection. When E. corrodens (3.8 X 10(7) CFU) was included in the inoculum, chronic lesions were established with a dose of 8.5 X 10(4) CFU of A. israelii. E. corrodens alone did not produce persistent lesions. Viable E. corrodens could be recovered from chronic mixed actinomycotic lesions in numbers that often equaled or exceeded the populations of A. israelii in the lesions. The duration of acute actinomycotic infections caused by A. viscosus was temporarily extended by the presence of E. corrodens. The cellular inflammatory response and overall morphology of mixed experimental lesions containing A. israelii and E. corrodens did not appear to be significantly different from those of pure-culture lesions containing A. israelii alone. E. corrodens cells could not be readily discerned in stained histological sections of mixed experimental lesions.
Comparing source coverage, citation counts and speed of indexing in Google Scholar and Scopus

An analysis of 1,200 target articles in 12 journals in 6 subject fields and of 7,000 citations to 36 top cited articles found in virology and chemistry a ratio of Google Scholar (GS) over Scopus citation counts between 0.8 and 1.5, in Chinese studies between 1.8 and 2.8, in computational linguistics between 2 and 4, and in political science journals between 3 and 4. Open access journals show higher ratios than their non-OA counterparts. Unique GS sources come from Google Books and/or from large book publishers, and from large disciplinary and institutional repositories. Unique Scopus sources are mainly books and Chinese journals. There is a huge dispersion in GS source titles and web links. The citation impact of documents in surplus sources covered in GS but not in Scopus and vice versa is some 80 per cent lower than that of documents in sources indexed in both. Pearson R between GS and Scopus citation counts at the article level are in all 12 target journals above 0.8, and for 8 journals above 0.9. Effect of double citation counts due to multiple citations with identical or substantially similar meta data occurs in less than 2 per cent of cases. In GS, the trade-off between data quality and indexing speed seems to be in favor of the latter. A median Scopus indexing delay of two months compared to GS is largely though not exclusively due to missing cited references in articles in press. Pros and cons of article-based and concept-based citation indexes are discussed.
Double‐barred galaxies at intermediate redshifts: a feasibility study

Despite the increasing number of studies of barred galaxies at intermediate and high redshifts, double-barred (S2B) systems have only been identified in the nearby (z <= 0.04) universe thus far. In this feasibility study, we demonstrate that the detection and analysis of S2Bs is possible at intermediate redshifts (0.1 less than or similar to z less than or similar to 0.5) with the exquisite resolution of the Hubble Space Telescope Advanced Camera for Surveys (HST/ACS). We identify barred galaxies in the HST/ACS data of the Great Observatories Origins Deep Survey (GOODS) using a novel method. The radial profile of the Gini coefficient - a model-independent structure parameter - is able to detect bars in early-type galaxies that are large enough that they might host an inner bar of sufficient angular size. Using this method and subsequent examination with unsharp masks and ellipse fits, we identified the two most distant S2Bs currently known (at redshifts z = 0.103 and 0.148). We investigate the underlying stellar populations of these two galaxies through a detailed colour analysis, in order to demonstrate the analysis that could be performed on a future sample of intermediate-redshift S2Bs. We also identify two S2Bs and five S2B candidates in the HST/ACS data of the Cosmic Evolution Survey (COSMOS). Our detections of distant S2Bs show that deep surveys like GOODS and COSMOS have the potential to push the limit for S2B detection and analysis out by a factor of 10 in redshift and look-back time (z approximate to 0.5, Delta t approximate to 5 Gyr) compared to the previously known S2Bs. This in turn would provide new insight into the formation of these objects.
Clogging of pervious concrete pile caused by soil piping: an approximate experimental study

Due to their high permeability and high strength, pervious concrete piles (PCPs) can improve ground bearing capacity. However, clogging of pervious concrete in practice is a potential disadvantage. To investigate the clogging mechanism of PCPs due to sand piping, a series of laboratory simulation tests is conducted on a developed hydraulic conductivity test system. This testing demonstrates the effects of pervious concrete porosity, grading of fine movable particles, mix ratio of skeleton particles to movable particles, relative density of soil, and distance between PCPs on PCP clogging. The experimental test results show that the hydraulic conductivity of PCP decreases for approximately 70 min and then becomes relatively stable. In addition, it is observed that PCP clogging rarely occurs in cases of low pervious concrete porosity, small movable sand particle size, high sand relative density, and large pile distance. The results also show that measurement of electrical conductivity can be an alternative method of hydraulic conductivity measurement. Based on the test results, preliminary clogging models are proposed.
Toward Trust and Reputation Based Web Service Selection : A Survey

Using trust and reputation mechanisms offers a promising way to solve the web service selection problem. The investigation of trust and reputation systems in other areas can provide valuable observations and approaches that can be used in web service systems. Therefore, this paper presents a systematic review of various trust and reputation systems and proposes a typology to classify them from three aspects, centralized vs. decentralized, persons/agents vs. resources, global vs. personalized. These aspects are important not only in that they clarify the difference between various existing trust and reputation systems, but also in that they point out the potential research directions for using trust and reputation in web services and provide some reference systems for them.