Miracle-dz/UniFAR-FTUs huggingface dataset:
Osaka Kyoiku University at NTCIR-10 CrossLink-2: Link Filtering by Title Tag of Corpus as a Dictionary

Our group (OKSAT) submitted two types of runs named SMP and REF for every subtasks of NTCIR-10 Cross-lingual Link Discovery (CLLD). Our method uses titles in Wikipedia pages (corpus) of source language as a entries of a dictionary, so no external dictionary is required. For SMP, we aimed to discover cross-lingual links of actual Wikipedia, in other words it targets Wikipedia ground truth. For REF, on the other hand, we aimed to discover as much meaningful cross-lingual links as possible automatically.
Characteristics of some new composite Right/Left-handed metamaterial transmission lines

This paper proposes a new composite right/left handed transmission line metamaterial with a series parallel LC circuit & a shunt series LC tank circuit. A shorted interdigital capacitor (IDC) provide the shunt series LC tank circuit, while the right handed parasitic series inductance & shunt series capacitance are generated by the metallic connections in the direction of propagation. A transmission line model & a full wave simulation are used to calculate the left handed inductance (LL) & capacitance (CL) values of the equivalent circuit of this structure.
Comparison of the theoretical and real-world evolutionary potential of a genetic circuit

With the development of next-generation sequencing technologies, many large scale experimental efforts aim to map genotypic variability among individuals. This natural variability in populations fuels many fundamental biological processes, ranging from evolutionary adaptation and speciation to the spread of genetic diseases and drug resistance. An interesting and important component of this variability is present within the regulatory regions of genes. As these regions evolve, accumulated mutations lead to modulation of gene expression, which may have consequences for the phenotype. A simple model system where the link between genetic variability, gene regulation and function can be studied in detail is missing. In this article we develop a model to explore how the sequence of the wild-type lac promoter dictates the fold-change in gene expression. The model combines single-base pair resolution maps of transcription factor and RNA polymerase binding energies with a comprehensive thermodynamic model of gene regulation. The model was validated by predicting and then measuring the variability of lac operon regulation in a collection of natural isolates. We then implement the model to analyze the sensitivity of the promoter sequence to the regulatory output, and predict the potential for regulation to evolve due to point mutations in the promoter region.
The Accuracy of Survival Time Prediction for Patients with Glioma Is Improved by Measuring Mitotic Spindle Checkpoint Gene Expression

Identification of gene expression changes that improve prediction of survival time across all glioma grades would be clinically useful. Four Affymetrix GeneChip datasets from the literature, containing data from 771 glioma samples representing all WHO grades and eight normal brain samples, were used in an ANOVA model to screen for transcript changes that correlated with grade. Observations were confirmed and extended using qPCR assays on RNA derived from 38 additional glioma samples and eight normal samples for which survival data were available. RNA levels of eight major mitotic spindle assembly checkpoint (SAC) genes (BUB1, BUB1B, BUB3, CENPE, MAD1L1, MAD2L1, CDC20, TTK) significantly correlated with glioma grade and six also significantly correlated with survival time. In particular, the level of BUB1B expression was highly correlated with survival time (p<0.0001), and significantly outperformed all other measured parameters, including two standards; WHO grade and MIB-1 (Ki-67) labeling index. Measurement of the expression levels of a small set of SAC genes may complement histological grade and other clinical parameters for predicting survival time.
Compact formulations as a union of polyhedra

We explore one method for finding the convex hull of certain mixed integer sets. The approach is to break up the original set into a small number of subsets, find a compact polyhedral description of the convex hull of each subset, and then take the convex hull of the union of these polyhedra. The resulting extended formulation is then compact, its projection is the convex hull of the original set, and optimization over the mixed integer set is reduced to solving a linear program over the extended formulation.The approach is demonstrated on three different sets: a continuous mixing set with an upper bound and a mixing set with two divisible capacities both arising in lot-sizing, and a single node flow model with divisible capacities that arises as a subproblem in network design.
Differential Expression of Group I Metabotropic Glutamate Receptors in Rat Spinal Cord Somatic and Autonomic Motoneurons: Possible Implications for the Pathogenesis of Amyotrophic Lateral Sclerosis

Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disorder characterized by the progressive loss of somatic, but not autonomic, motoneurons. The reason for this selective vulnerability is unknown. The pathogenesis of ALS is thought to involve glutamatergic excitotoxic mechanisms. While overactivation of ionotropic glutamate receptors may trigger excitotoxicity, we have previously shown that stimulation of group I metabotropic glutamate receptors (mGluRs) can exert neuroprotective effects on cultured motoneurons. Using in situ hybridization, we found a differential expression of group I mGluRs (mGluR1 and 5) in rat spinal cord. Autonomic motoneurons from the sacral parasympathetic Onuf's nucleus and thoracic sympathetic neurons, which are spared in ALS, express high levels of mGluR5, while somatic motoneurons do not. In addition, mGluR1 mRNA is found only in smaller somatic motoneurons, which seem to be less vulnerable in ALS. Thus, differential mGluR expression might provide a possible clue to the selective vulnerability of different motoneuronal subpopulations in ALS.
Bacterial meningitis in Finland, 1995–2014: a population-based observational study

Objectives Bacterial meningitis remains an important cause of morbidity and mortality worldwide. Its epidemiological characteristics, however, are changing due to new vaccines and secular trends. Conjugate vaccines against Haemophilus influenzae type b and Streptococcus pneumoniae (10-valent) were introduced in 1986 and 2010 in Finland. We assessed the disease burden and long-term trends of five common causes of bacterial meningitis in a population-based observational study. Methods A case was defined as isolation of S. pneumoniae, Neisseria meningitidis, Streptococcus agalactiae, Listeria monocytogenes or H. influenzae from cerebrospinal fluid and reported to national, population-based laboratory surveillance system during 1995–2014. We evaluated changes in incidence rates (Poisson or negative binomial regression), case fatality proportions (χ2) and age distribution of cases (Wilcoxon rank-sum). Results During 1995–2014, S. pneumoniae and N. meningitidis accounted for 78% of the total 1361 reported bacterial meningitis cases. H. influenzae accounted for 4% of cases (92% of isolates were non-type b). During the study period, the overall rate of bacterial meningitis per 1 00 000 person-years decreased from 1.88 cases in 1995 to 0.70 cases in 2014 (4% annual decline (95% CI 3% to 5%). This was primarily due to a 9% annual reduction in rates of N. meningitidis (95% CI 7% to 10%) and 2% decrease in S. pneumoniae (95% CI 1% to 4%). The median age of cases increased from 31 years in 1995–2004 to 43 years in 2005–2014 (p=0.0004). Overall case fatality proportion (10%) did not change from 2004 to 2009 to 2010–2014. Conclusions Substantial decreases in bacterial meningitis were associated with infant conjugate vaccination against pneumococcal meningitis and secular trend in meningococcal meningitis in the absence of vaccination programme. Ongoing epidemiological surveillance is needed to identify trends, evaluate serotype distribution, assess vaccine impact and develop future vaccination strategies.
Criterion Setting and the Dynamics of Recognition Memory

Models of recognition memory have traditionally struggled with the puzzle of criterion setting, a problem that is particularly acute in cases in which items for study and test are of widely varying types, with differing degrees of baseline familiarity and experience (e.g., words vs. random dot patterns). We present a dynamic model of the recognition process that addresses the criterion setting problem and produces joint predictions for choice and reaction time. In this model, recognition decisions are based not on the absolute value of familiarity, but on how familiarity changes over time as features are sampled from the test item. Decisions are the outcome of a race between two parallel accumulators: one that accumulates positive changes in familiarity (leading to an ''old'' decision) and another that accumulates negative changes (leading to a ''new'' decision). Simulations with this model make realistic predictions for recognition performance and latency regardless of the baseline familiarity of study and test items.
Chronic Production of Angiotensin IV in the Brain Leads to Hypertension That Is Reversible With an Angiotensin II AT1 Receptor Antagonist

Angiotensin IV (Ang IV) is a metabolite of the potent vasoconstrictor angiotensin II (Ang II). Because specific binding sites for this peptide have been reported in numerous tissues including the brain, it has been suggested that a specific Ang IV receptor (AT4) might exist. Bolus injection of Ang IV in brain ventricles has been implicated in learning, memory, and localized vasodilatation. However, the functions of Ang IV in a physiological context are still unknown. In this study, we generated a transgenic (TG) mouse model that chronically releases Ang IV peptide specifically in the brain. TG mice were found to be hypertensive by the tail-cuff method as compared with control littermates. Treatment with the angiotensin-converting enzyme inhibitor captopril had no effect on blood pressure, but surprisingly treatment with the Ang II AT1 receptor antagonist candesartan normalized the blood pressure despite the fact that the levels of Ang IV in the brains of TG mice were only 4-fold elevated over the normal endogenous level of Ang peptides. Calcium mobilization assays performed on cultured CHO cells chronically transfected with the AT1 receptor confirm that low-dose Ang IV can mobilize calcium via the AT1 receptor only in the presence of Ang II, consistent with an allosteric mechanism. These results suggest that chronic elevation of Ang IV in the brain can induce hypertension that can be treated with angiotensin II AT1 receptor antagonists.
The Yeast Epsin Ent1 Is Recruited to Membranes through Multiple Independent Interactions*

In addition to its well known role in targeting proteins for proteasomal degradation, ubiquitin (Ub) is also involved in promoting internalization of cell surface proteins into the endocytic pathway. Moreover, putative Ub interaction motifs (UIMs) as well as Ub-associated (UBA) domains have been identified in key yeast endocytic proteins (the epsins Ent1 and Ent2, and the Eps15 homolog Ede1). In this study, we characterized the interaction of Ub with the Ede1 UBA domain and with the UIMs of Ent1. Our data suggest that the UIMs and the UBA are involved in binding these proteins to biological membranes. We also show that the Ent1 ENTH domain binds to phosphoinositides in vitro and that Ent1 NPF motifs interact with the EH domain-containing proteins Ede1 and Pan1. Our findings indicate that the ENTH domain interaction with membrane lipids cooperates with the binding of membrane-associated Ub moieties. These events may in turn favor the occurrence of other interactions, for instance EH-NPF recognition, thus stabilizing networks of low affinity binding partners at endocytic sites.
Urinary Incontinence in Women: Variation in Prevalence Estimates and Risk Factors

OBJECTIVE: To understand variation in prevalence of urinary incontinence (UI) and risk factors, given different definitions. METHODS: The National Health and Nutrition Examination Survey 2001–2002 data on UI were used. Prevalence, severity, and associated risk factors of stress, urge, mixed, and any UI were estimated in 2,875 adult women. Severe UI was defined as incontinence a few times or more per week. Moderate UI was defined as an incontinence frequency of a few times per month only, and mild UI was defined as incontinence frequency of a few times per year only. Odds ratios for the association of potential risk factors were examined in a logistic regression model. RESULTS: The overall prevalence of stress, urge, mixed, and any UI was 23.7%, 9.9%, 14.5%, and 49.2%, respectively. Prevalence of stress UI peaked at the fifth decade. Prevalence of urge and mixed UI increased with age. The largest number of risk factors and the strongest associations were found with severe UI. Age, ethnic background, and weight were significant risk factors common to all UI severity levels. Although parity and hysterectomy were risk factors for moderate and severe UI, they were not for mild UI. CONCLUSION: Prevalence of UI varies substantially by type and case definition. The stronger associations of known risk factors with severe UI and the lack of risk factors with lesser UI severity types suggest that severe UI includes primarily clinically significant cases, whereas mild UI represents transient or nonpathologic states that may not be clinically significant. LEVEL OF EVIDENCE: III
Assessing ecological effects of glacial meltwater on lakes fed by the Greenland Ice Sheet: The role of nutrient subsidies and turbidity

ABSTRACT Meltwater discharge from the Greenland Ice Sheet (GrIS) exports sediment, solutes, total phosphorus (TP), dissolved inorganic nitrogen (DIN), and other macro- and micronutrients to associated aquatic ecosystems. It remains unclear how this meltwater affects the ecology of glacially fed (GF) lakes. We assessed a suite of physical, chemical, and biological features of four GF lakes, and compared them to those of four nearby snow- and groundwater-fed (SF) lakes. We found that TP concentrations were six times higher in GF compared to SF lakes, but microbial extracellular enzyme activities and aluminum, iron, and phosphorus sediment fractions suggested that much of this TP in GF lakes is likely not biologically available. Turbidity was fifteen times higher in GF lakes, and DIN was twice as high than in SF lakes, but these nitrogen differences were not significant. While diatom species richness did not significantly differ between lake types, GF lakes had higher water column chlorophyll a (Chl a). Diatom species distributions across all lakes were strongly associated with turbidity, TP, and dissolved organic carbon (DOC). While cosmopolitan diatom taxa such as Discostella stelligera were found in both lake types, diatom communities differed across lake types. For instance, Fragilaria and Psammothidium species dominated GF lakes, while Achnanthes species and Lindavia ocellata were dominant in SF lakes. In addition to turbidity, the moderate amounts of DIN in GF lakes may play an important role in shaping diatom communities. This is supported by the high abundance in GF lakes of taxa such as Fragilaria tenera and D. stelligera, which reflect nitrogen enrichment in some lakes. Our results demonstrate how GrIS meltwaters alter the ecology of Arctic lakes, and contribute to the growing body of literature that reveals spatial variability in the effects of glacial meltwaters on lake ecosystems.
Reshaping automatic speech transcripts for robust high-level spoken document analysis

High-level spoken document analysis is required in many applications seeking access to the semantic content of audio data, such as information retrieval, machine translation or automatic summarization. It is nevertheless a difficult task that is generally based on transcripts provided by an automatic speech recognition system. Unlike standard texts, transcripts belong to the category of highly noisy data because of word recognition errors that affect, in particular, very significant words such as named entities (e.g. person's names, locations, organizations). Transcripts also contain specificities of spoken language that make ineffective their processing by natural language processing tools designed for texts. To overcome these issues, this paper proposes a method to reshape automatic speech transcripts for robust high-level spoken document analysis. The method consists in conceiving a new word-level confidence measure that may efficiently ensure the reliability of transcribed words, focusing on words that are relevant for high-level spoken document analysis such as named entities. The approach consists in combining different features collected from various sources of knowledge thanks to a machine learning method based on conditional random fields. In addition to standard features (morphosyntactic, linguistic and phonetic), we introduce new semantic features based on the decisions of three robust named entity recognition systems to better estimate the reliability of named entities. Experiments, conducted on the French broadcast news corpus ESTER, demonstrate the added-value of the proposed word-level confidence measure for error detection and named entity recognition, with respect to the basic confidence measure provided by an automatic speech recognition system.
Transhepatic perforation of the gallbladder: rare complication of a common disease

Acute cholecystitis leading to gallbladder perforation is relatively common. However, transhepatic perforation of the gallbladder leading to biliary peritonitis is very rare. We present a rare case of biliary peritonitis caused by transhepatic perforation of the gallbladder.
Management of patients with idiopathic pulmonary fibrosis in clinical practice: the INSIGHTS-IPF registry

After introduction of the new international guidelines on idiopathic pulmonary fibrosis (IPF) in 2011, we investigated clinical management practices for patients with IPF according to physicians' diagnoses. A prospective, multicenter, noninterventional study with comprehensive quality measures including on-site source data verification was performed in Germany. 502 consecutive patients (171 newly diagnosed, 331 prevalent; mean±sd age 68.7±9.4 years, 77.9% males) with a mean disease duration of 2.3±3.5 years were enrolled. IPF diagnosis was based on clinical assessments and high-resolution computed tomography (HRCT) in 90.2%, and on surgical lung biopsy combined with histology in 34.1% (lavage in 61.8%). The median 6-min walk distance was 320 m (mean 268±200 m). The mean forced vital capacity was 72±20% pred and diffusing capacity of the lung for carbon monoxide was 35±15% pred. No drugs were administered in 17.9%, oral steroids in 23.7%, N-acetylcysteine in 33.7%, pirfenidone in 44.2% and other drugs in 4.6% of patients. Only 2.8% of the cohort was listed for lung transplantation. IPF patients were diagnosed in line with the new guidelines. They had more severe disease than those enrolled in recent randomised controlled trials. In addition to HRCT, the frequency of lung biopsies was surprisingly high. Treatment patterns varied substantially. This largest published registry of IPF patients shows surprising disease severity and treatment variation http://ow.ly/JbWRn
Accurate Phylogenetic Tree Reconstruction from Quartets: A Heuristic Approach

Supertree methods construct trees on a set of taxa (species) combining many smaller trees on the overlapping subsets of the entire set of taxa. A ‘quartet’ is an unrooted tree over taxa, hence the quartet-based supertree methods combine many -taxon unrooted trees into a single and coherent tree over the complete set of taxa. Quartet-based phylogeny reconstruction methods have been receiving considerable attentions in the recent years. An accurate and efficient quartet-based method might be competitive with the current best phylogenetic tree reconstruction methods (such as maximum likelihood or Bayesian MCMC analyses), without being as computationally intensive. In this paper, we present a novel and highly accurate quartet-based phylogenetic tree reconstruction method. We performed an extensive experimental study to evaluate the accuracy and scalability of our approach on both simulated and biological datasets.
The cause and consequence of ontogenetic changes in social aggregation in New Zealand spiny lobsters

Ontogenetic changes in the behavior, spatial distribution, or habitat use of a species are presumably adaptations to ecological forces that differ in their effect on various life stages. The New Zealand rock lobster Jasus edwardsii is one of several species of spiny lobster that exhibits dramatic ontogenetic shifts in sociality and spatial distribution, and we tested whether such changes are adaptive. We first surveyed several natural populations of J. edwardsii to document size-specific differences in aggregation. To determine if chemical cues discharged by conspecifics promote aggregation of certain ontogenetic stages, we tested the responsiveness of lobsters of 3 ontogenetic stages (early benthic juvenile, juvenile, and subadult) to the chemical cues produced by conspecifics of different sizes. Finally, we tethered lobsters of different ontogenetic stages alone and in groups to test the effect of lobster size and aggregation on mortality. Our results offer compelling evidence that pre-reproductive J. edwardsii undergo an ontogenetic change in sociality that alters their spatial distribution and survival. Our field surveys show that J. edwardsii are solitary as early benthic juveniles and become social and aggregate as they grow larger. We then demonstrate, using laboratory experiments, that there is a size-specific increase in the response of pre-reproductive J. edwardsii to the chemical cues of larger conspecifics which facilitates these ontogenetic changes in aggregation. Finally, our tethering results confirm that this change in social condition is selectively advantageous: aggregation does not increase the survival of small lobsters, but larger lobsters survive better in groups. Thus, in this study we demonstrate the linkage between ontogenetic changes in the spatial distribution of a species, the behavioral process that creates the pattern, and the selective advantage conferred by these developmental changes.