Miracle-dz/UniFAR-FTUs huggingface dataset:
Citations increase with manuscript length, author number, and references cited in ecology journals

Abstract Most top impact factor ecology journals indicate a preference or requirement for short manuscripts; some state clearly defined word limits, whereas others indicate a preference for more concise papers. Yet evidence from a variety of academic fields indicates that within journals longer papers are both more positively reviewed by referees and more highly cited. We examine the relationship between citations received and manuscript length, number of authors, and number of references cited for papers published in 32 ecology journals between 2009 and 2012. We find that longer papers, those with more authors, and those that cite more references are cited more. Although paper length, author count, and references cited all positively covary, an increase in each independently predicts an increase in citations received, with estimated relationships positive for all the journals we examined. That all three variables covary positively with citations suggests that papers presenting more and a greater diversity of data and ideas are more impactful. We suggest that the imposition of arbitrary manuscript length limits discourages the publication of more impactful studies. We propose that journals abolish arbitrary word or page limits, avoid declining papers (or requiring shortening) on the basis of length alone (irrespective of content), and adopt the philosophy that papers should be as long as they need to be.
Mental health consumer and caregiver perceptions of stigma in Australian community pharmacies

Background: The stigma of mental illness can be a barrier to effective medication management in the community pharmacy setting. This article explored mental health consumers’ or caregivers’ experiences of stigma in Australian community pharmacies. Materials: Semi-structured interviews and focus groups were conducted with a purposive sample of consumers or caregivers (n = 74). Interview transcripts were analysed using a general inductive approach. Discussion: Stigma presented a barrier to effective mental health management. Self-stigma impeded consumers’ community pharmacy engagement. Positive relationships with knowledgeable staff are fundamental to reducing stigma. Conclusions: Findings provide insight into the stigma of mental illness in community pharmacies.
Malignant pleural effusion cell blocks are substitutes for tissue in EML4‐ALK rearrangement detection in patients with advanced non‐small‐cell lung cancer

To evaluate the feasibility of malignant pleural effusions (MPE) as surrogate samples for the detection of echinoderm microtubule‐associated protein‐like4 (EML4)‐anaplastic lymphoma kinase (ALK) and to investigate the prognostic and predictive value of EML4‐ALK in MPE of non‐small‐cell lung cancer (NSCLC).
Initializing sea ice thickness and quantifying uncertainty in seasonal forecasts of Arctic sea ice

Arctic sea ice has undergone a dramatic transformation in recent decades, including a substantial reduction in sea ice extent in summer months. Such changes, combined with relatively recent advancements in seasonal (1-12 months) to decadal forecasting, have prompted a rapidly-growing body of research on forecasting Arctic sea ice on seasonal timescales. These forecasts are anticipated to benefit a vast array of endusers whose activities are dependent on Arctic sea ice conditions. The research goal of this thesis is to address fundamental challenges pertaining to seasonal forecasts of Arcitc sea ice, with a particular focus placed on improving operational sea ice forecasts in the Canadian Seasonal to Interannual Prediction System (CanSIPS). Seasonal forecasts are strongly dependent on the accuracy of observations used as initial condition inputs. A key challenge initializing Arctic sea ice is the sparse availability of Arctic sea ice thickness (SIT) observations. I present on the development of three statistical models that can be used for estimating Arctic SIT in real time for sea ice forecast initialization. The three statistical models are shown to vary in their ability to capture the recent thinning of sea ice, as well as their ability to capture interannual variations in SIT anomalies; however, each of the models is shown to dramatically improve the representation of SIT compared to the climatological SIT estimates used to initialize CanSIPS. I conduct a thorough assessment of sea ice hindcast skill using the Canadian Climate Model, version 3 (one of two models used in CanSIPS), in which the dependence of hindcast skill on SIT initialization is investigated. From this assessment, it can be concluded that all three statistical models are able to estimate SIT sufficiently to improve hindcast skill relative to the climatological initialization. However, the accuracy with which the initialization fields represent both the thinning of the ice pack over time and interannual variability impacts predictive skill for pan-Arctic sea ice area (SIA) and regional sea ice concentration (SIC), with the most robust improvements obtained with two statistical models that adequately represent both processes. The final goal of this thesis is to improve the quantification of uncertainty in seasonal forecasts of regional Arctic sea ice coverage. Information regarding forecast uncertainty is crucial for end-users who want to quantify the risk associated with trusting a particular forecast. I develop statistical post-processing methodology for improving probabilistic forecasts of Arctic SIC. The first of these improvements is intended to reduce sampling uncertainty by fitting ensemble SIC forecasts to a para-
Monotonic and cyclic behaviors of loose anisotropically consolidated calcareous sand in torsional shear tests

ABSTRACT The behavior of loose anisotropically consolidated calcareous sand obtained from an island in the South China Sea was investigated under undrained monotonic and cyclic loading in a hollow cylinder torsional apparatus. The tests were conducted on specimens which consolidated under various initial effective confining pressures and consolidation stress ratios. The monotonic test results show that the failure and phase transformation line are essentially independent of the consolidation conditions, while the initial contractive tendency of the specimens decreases with an increasing consolidation stress ratio. During monotonic loading of the anisotropically consolidated specimens, a same major principal stress direction is observed at the constant stress ratio lines up to the phase transformation line, irrespective of initial effective confining pressure. The cyclic strength of the sand increases with an increasing consolidation stress ratio. Moreover, a pronounced stress dependence is observed in the sand with higher consolidation stress ratio. During cyclic loading, the generated excess pore water pressure presents considerable fluctuations. The normalized terminal excess pore water pressure is described as a function of consolidation stress ratio. The tests show that the particle shape, rather than particle crushing, plays an important role in the monotonic and cyclic behaviors of the calcareous sand.
Modulators of Very Low Voriconazole Concentrations in Routine Therapeutic Drug Monitoring

Very low voriconazole concentrations are commonly observed during therapeutic drug monitoring. Possible mechanisms include inappropriate dose selection, rapid metabolism (as a result of genetic polymorphisms or enzyme induction), and also nonadherence. We aimed to develop a method to distinguish between rapid metabolism of and nonadherence to voriconazole by quantification of voriconazole metabolites. In addition, the relevance of common genetic polymorphisms of CYP2C19 was assessed. In a retrospective study, samples with voriconazole concentrations 0.2 μg/mL or less in routine therapeutic drug monitoring (as quantified by high-performance liquid chromatography) were evaluated. Voriconazole and its N-oxide metabolite were quantified in residual blood using a highly sensitive liquid chromatography-tandem mass spectroscopy method (lower limit of quantitation = 0.03 μg/mL). Genetic polymorphisms of CYP2C19 were determined by real-time polymerase chain reaction using the hybridization probe format and the polymerase chain reaction-random fragment length polymorphism format. A total of 747 routine therapeutic drug monitoring plasma/blood samples of 335 patients treated with systemic voriconazole were analyzed and in 18.7% of all samples, voriconazole concentrations 0.2 μg/mL or less were found. In 32 samples (30 patients) with adequate dosage and timing of blood withdrawal, nonadherence was strongly suspected in seven patients because voriconazole-N-oxide concentrations were below 0.03 μg/mL, which was not observed in a reference group of 51 healthy volunteers with controlled drug intake. In 10 patients, of whom EDTA blood was available, the ultrarapid metabolizer genotype (CYP2C19*1\*17, CYP2C19*17\*17) was found in 80% and its prevalence was significantly higher as compared to a reference group (P = 0.02). In conclusion, quantification of voriconazole-N-oxide allowed for detection of suspected nonadherence in one of four patients with very low voriconazole concentrations. In the remaining patients, ultrarapid metabolism resulting from the CYP2C19*17 polymorphism appears to play a major role. Thus, in the case of voriconazole therapy failure, both nonadherence and genetic factors have to be considered.
Prolonged cortical silent period after transcranial magnetic stimulation in generalized epilepsy.

silent period after transcranial magnetic stimulation in generalized epilepsy Article abstract—Transcranial magnetic stimulation (TMS) produces a cortical silent period (CSP) during a voluntary contraction. The duration of the CSP was used to assess the level of intracortical inhibition in patients with untreated idiopathic generalized epilepsy (IGE). Mean CSP duration was assessed at three TMS stimuli in 21 patients with IGE compared with 19 normal control subjects. Mean CSP duration was increased at all stimulus intensities, indicating that intracortical inhibition is increased in patients with IGE.
Functional Characteristics of the Gut Microbiome in C57BL/6 Mice Differentially Susceptible to Plasmodium yoelii

C57BL/6 mice are widely used for in vivo studies of immune function and metabolism in mammals. In a previous study, it was observed that when C57BL/6 mice purchased from different vendors were infected with Plasmodium yoelii, a causative agent of murine malaria, they exhibited both differential immune responses and significantly different parasite burdens: these patterns were reproducible when gut contents were transplanted into gnotobiotic mice. To gain insight into the mechanism of resistance, we removed whole ceca from mice purchased from two vendors, Taconic Biosciences (low parasitemia) and Charles River Laboratories (high parasitemia), to determine the combined host and microflora metabolome and metatranscriptome. With the exception of two Charles River samples, we observed ≥90% similarity in overall bacterial gene expression within vendors and ≤80% similarity between vendors. In total 33 bacterial genes were differentially expressed in Charles River mice (p-value < 0.05) relative to the mice purchased from Taconic. Included among these, fliC, ureABC, and six members of the nuo gene family were overrepresented in microbiomes susceptible to more severe malaria. Moreover, 38 mouse genes were differentially expressed in these purported genetically identical mice. Differentially expressed genes included basigin, a cell surface receptor required for P. falciparum invasion of red blood cells. Differences in metabolite pools were detected, though their relevance to malaria infection, microbial community activity, or host response is not yet understood. Our data have provided new targets that may connect gut microbial activity to malaria resistance and susceptibility phenotypes in the C57BL/6 model organism.
One Signal, Multiple Pathways: Diversity Comes from the Receptor

Type “Wnt” into Google Scholar, and you'll get nearly 72,000 hits, revealing the pivotal role this widely conserved family of signaling proteins plays in development and disease. Wnt proteins trigger complex signaling cascades that regulate cell growth, migration, differentiation, and many other aspects of development with the help of numerous interacting components. In the best-understood, “canonical” pathway, Wnt signaling molecules (called ligands) bind simultaneously to two coreceptors on the cell surface (Frizzled and LRP), allowing β-catenin proteins to stabilize (avoid destruction), enter the nucleus, associate with the transcription factor complex TCF/LEF, and activate genes involved in cell survival, proliferation, or differentiation. Inappropriate activation of β-catenin has been linked to several types of cancer.
Changes of Surface Composition and Morphology after Incorporation of Ions into Biomimetic Apatite Coating

Fabrication of trace elements incorporated apatite coating could combine the ions’ pharmaceutical effect into the materials. In this study, strontium, silicon, and fluoride ions have been incorporated into apatite coatings through a biomineralization method, which mimics an in vitro mineralization process. The surface composition is tested with X-ray diffraction and X-ray photoelectron spectroscopy, and the surface morphology is characterized with scanning electron microscopy. Compared with pure hydroxyapatite coating, the strontium, silicon, and fluoride substituted apatite coatings show different morphology as spherical, needle-like, and nano-flake-like, individually. The crystal size of these biomimetic hydroxyapatite coatings decreased after ion substitution. The results of the analysis of surface composition present the ion substitutions are increased with the increasing of ion concentrations in the soaking solution. That means the ion incorporation into the apatite structure based on the biomineralization method could not only vary the ion content in but also change the morphology of the apatite coatings. Herein, the role of ion substitution is considered from the point of view of materials science at the micro structural and surface chemistry levels.
A comparative study of the effect of parameter scalability in multi-objective metaheuristics

Some real-world optimization problems have hundreds or even thousands of decision variables. However, the effect that the scalability of parameters has in modern multi-objective metaheuristic algorithms has not been properly studied (the current benchmarks are normally adopted with ten to thirty decision variables). In this paper, we adopt a benchmark of parameter-wise scalable problems (the ZDT test problems) and analyze the behavior of six multi-objective metaheuristics on these test problems when using a number of decision variables that goes from 8 up to 2048. The computational effort required by each algorithm in order to reach the true Pareto front is also analyzed. Our study concludes that a particle swarm algorithm provides the best overall performance, although it has difficulties in multifrontal problems.
The Brain Ages Optimally to Model Its Environment: Evidence from Sensory Learning over the Adult Lifespan

The aging brain shows a progressive loss of neuropil, which is accompanied by subtle changes in neuronal plasticity, sensory learning and memory. Neurophysiologically, aging attenuates evoked responses—including the mismatch negativity (MMN). This is accompanied by a shift in cortical responsivity from sensory (posterior) regions to executive (anterior) regions, which has been interpreted as a compensatory response for cognitive decline. Theoretical neurobiology offers a simpler explanation for all of these effects—from a Bayesian perspective, as the brain is progressively optimized to model its world, its complexity will decrease. A corollary of this complexity reduction is an attenuation of Bayesian updating or sensory learning. Here we confirmed this hypothesis using magnetoencephalographic recordings of the mismatch negativity elicited in a large cohort of human subjects, in their third to ninth decade. Employing dynamic causal modeling to assay the synaptic mechanisms underlying these non-invasive recordings, we found a selective age-related attenuation of synaptic connectivity changes that underpin rapid sensory learning. In contrast, baseline synaptic connectivity strengths were consistently strong over the decades. Our findings suggest that the lifetime accrual of sensory experience optimizes functional brain architectures to enable efficient and generalizable predictions of the world.
TORC1 Regulates Pah1 Phosphatidate Phosphatase Activity via the Nem1/Spo7 Protein Phosphatase Complex

The evolutionarily conserved target of rapamycin complex 1 (TORC1) controls growth-related processes such as protein, nucleotide, and lipid metabolism in response to growth hormones, energy/ATP levels, and amino acids. Its deregulation is associated with cancer, type 2 diabetes, and obesity. Among other substrates, mammalian TORC1 directly phosphorylates and inhibits the phosphatidate phosphatase lipin-1, a central enzyme in lipid metabolism that provides diacylglycerol for the synthesis of membrane phospholipids and/or triacylglycerol as neutral lipid reserve. Here, we show that yeast TORC1 inhibits the function of the respective lipin, Pah1, to prevent the accumulation of triacylglycerol. Surprisingly, TORC1 regulates Pah1 in part indirectly by controlling the phosphorylation status of Nem1 within the Pah1-activating, heterodimeric Nem1-Spo7 protein phosphatase module. Our results delineate a hitherto unknown TORC1 effector branch that controls lipin function in yeast, which, given the recent discovery of Nem1-Spo7 orthologous proteins in humans, may be conserved.
Premorbid self‐disorders and lifetime diagnosis in the schizophrenia spectrum: a prospective high‐risk study

The notion of a disordered self as a core disturbance of schizophrenia was proposed in many foundational texts. Recent studies, spurred by the development of the Examination of Anomalous Self‐Experience (EASE), seem to indicate that self‐disorders are a specific manifestation of schizophrenia vulnerability. Follow‐up studies of help‐seeking, prodromal and first‐admission patients have demonstrated the utility of self‐disorders for predicting later schizophrenia‐spectrum disturbance. We wished to extend these findings by gauging the predictive value of self‐disorders in a premorbid, non‐clinical population at high risk for schizophrenia.
Neurological complications in AIDS patients receiving HAART: a 2‐year retrospective study

The positive role of highly active anti‐retroviral therapy (HAART) in reducing opportunistic infections in acquired immunodeficiency syndrome (AIDS) patients is well known. However, case reports from around the world have demonstrated that some patients seem to suffer a paradoxical deterioration of health as their immune function improves with treatment. This phenomenon has been called immune restoration inflammatory syndrome (IRIS). In northern Thailand, GPO‐vir (Stavudine‐D4T + Lamivudine‐3TC + Nevirapine‐NVP) has been promoted for the treatment of AIDS patients since April 2002, in accordance with the Government Pharmaceutical Organization's guidelines. However, the incidence rates of IRIS affecting nervous system (NIRIS) and non‐NIRIS in comparison with the previous incidence of AIDS‐defining disease have not been reported. We conducted a retrospective study to review the incidence of NIRIS and non‐NIRIS in AIDS patients treated with GPO‐vir in Chiang Mai University Hospital, Thailand, between May 2002 and April 2004. We compare these incidence rates with the incidence rates of neurological complications in the pre‐HAART era. Altogether 506 AIDS patients were treated with GPO‐vir during the specified period. The overall incidence of NIRIS, including progressive multifocal leukoencephalopathy (PML), cerebral toxoplasmosis and cytomegalovirus (CMV) retinitis, was lower than the previous incidence of AIDS‐defining disease in the pre‐HAART era. However, the incidence of ischemic stroke, hemorrhagic stroke and primary central nervous system (CNS) lymphoma had increased.
A new multitask learning method for multiorganism gene network estimation

A new method for multitask learning in a Bayesian network context is presented for multiorganism gene network estimation. When the input datasets are sparse, as is the case in microarray gene expression data, it becomes difficult to separate random correlations from actual edges in the true underlying Bayesian network. Multitask learning takes advantage of the similarity between related tasks, in order to construct a more accurate model of the underlying relationships represented by the Bayesian networks. The proposed method is tested on synthetic data to illustrate its validity. Then it is iteratively applied on real gene expression data to learn the genetic regulatory networks of two organisms with homologous genes (human and yeast).
Stubborn Mining: Generalizing Selfish Mining and Combining with an Eclipse Attack

Selfish mining, originally discovered by Eyal et al. [9], is a well-known attack where a selfish miner, under certain conditions, can gain a disproportionate share of reward by deviating from the honest behavior. In this paper, we expand the mining strategy space to include novel "stubborn" strategies that, for a large range of parameters, earn the miner more revenue. Consequently, we show that the selfish mining attack is not (in general) optimal. Further, we show how a miner can further amplify its gain by non-trivially composing mining attacks with network-level eclipse attacks. We show, surprisingly, that given the attacker's best strategy, in some cases victims of an eclipse attack can actually benefit from being eclipsed!
Eemian to Early Weichselian organic deposits in the watershed kettle-hole basins in central Poland

In the examined part of central Poland, there are numerous kettle-hole basins filled with mineral and biogenic sediments of the Eemian Interglacial and Early Weichselian. These basins are located in varied geological and geomorphological locations with variable thicknesses of the sediments and deposits. The infillings were investigated by lithological and palaeobotanic methods. Lithology of the biogenic sediments is diverse, primarily gyttja and peat, but also organic silt. A number of the documented sites contain a record of environmental changes throughout the glacial-interglacial cycle from the end of the Warta Stadial (Saalian) to Early Weichselian. Local geological, geomorphological and hydrological conditions influenced the possibility of continuous peat-lake accumulation and the timing of the completion of this accumulation. Biogenic sediments are covered with the Middle and Late Weichselian mineral sediments which indicate climatic changes and are the main reason for rapid and synchronic degradation of kettle-hole infillings.