Miracle-dz/UniFAR-FTUs huggingface dataset:
Draft Genome Sequence of Lactobacillus mali KCTC 3596

ABSTRACT We announce the draft genome sequence of the type strain Lactobacillus mali KCTC 3596 (2,652,969 bp, with a G+C content of 36.0%), which is one of the most prevalent lactic acid bacteria present during the manufacturing process of apple juice. The genome consists of 122 large contigs (>100 bp). All of the contigs were assembled by Newbler Assembler 2.3 (454 Life Science).
Multilevels Hidden Markov Models For Temporal Data Mining

This paper describes new temporal data mining techniques for extracting information from temporal health records consisting of time series of diabetic patients’ treatments. In this new method, there are three steps for analyzing patterns from a longitudinal data set. The first step, a structural-based pattern search, to find qualitative patterns (or, structural patterns). The second step performs a value-based search to find quantitative patterns. In the third step we combine results from the first two steps to form new model. The hidden Markov model has the expressive power of both qualitative analysis and data quantitative analysis. The global patterns can therefore be identified from a DTS set.
Values and Display Rules for Specific Emotions

Based on the CAD Triad Hypothesis (Rozin, Lowery, Imada, & Haidt, 1999), the authors hypothesized relationships between specific values and display rules for specific emotions. In particular, the authors proposed that Conservation and Self-Enhancement would be related to the display rule to express contempt, Conservation would be related to the display rule to express disgust, and Openness to Change and Self-Transcendence would be related to the display rules to express anger and sadness. To test this framework and its cross-cultural applicability, the present study examines values and emotional display rules among 106 U.S. Americans and 77 Germans. As predicted, Americans valued Conservation and Self-Enhancement more than did Germans, who valued Openness to Change and Self-Transcendence more than did Americans. These value differences were associated with differences in display rules; Americans endorsed contempt and disgust expressions more than did Germans, who endorsed anger and sadness expressions more than did Americans. Values mediated (“unpackaged”) many of these country differences in display rules. Implications of these findings are discussed.
The early development of muscle spindles in the rat.

The morphogenesis of muscle spindles in rat lower hind-limb muscles has been investigated using the electron microscope. The earliest detectable spindles are seen in the 19.5-day foetus and consist of a single myotube bearing simple nerve terminals of the large primary afferent axon from nearby unmyelinated intramuscular nerve trunks. The capsule forms by an extension of the perineural epithelium of the supplying nerve fasciculus, and is confined initially to the innervated zone. Myonuclei accumulate in this region, so that the first intrafusal muscle fibre to develop is a nuclear-bag fibre. Myoblasts, present within the capsule of the spindle throughout its development, fuse to form a smaller less-differentiated myotube by the 20-day foetal stage. This new myotube matures by close association with the initial fibre, and by birth (21-22 days gestation) has formed the smaller, intermediate bag fibre, that has been identified histochemically and ultrastructurally in the adult. The nuclear-chain fibres develop in the same way; myoblasts fuse to form satellite myotubes that mature in pseudopodial apposition to one of the other fibres within its basement membrane. This apposition consists of extensions of sarcoplasm from the developing myotube into the supporting fibre. By the 4-day postnatal stage the full adult complement of 4 intrafusal muscle fibres is present, although ultrastructural variations, seen in the adult, are not differentiated. The fusimotor innervation begins to arrive at birth, but is not mature until the 12th postnatal day, when the myofibrillar ultrastructural differentiation, including the loss of the M-line in the large-diameter bag fibre, is complete. The periaxial space appears at the same time. It is suggested that the sequential development of the intrafusal fibres is a reflexion of the decreasing morphogenetic effect of the afferent innervation, whereas the role of the fusimotor innervation is in ultrastructural, myofibrillar differentiation.
Adaptation: A Two-Perception Probabilistic Conceptual Framework

We introduce a two-perception probabilistic concept of adaptation (TPPCA), which accounts for fast and slow adaptation processes. The outcome of both processes depends on the perceptual difference (termed herein a quantum) of how an individual perceives his or her abilities, skills, and capacities (βv) to interact, cope, and perform a given task (δi). Thus, the adaptation process is determined by (βv – δi). Fast adaptation processes target aspects that require immediate responses while slow adaptation processes involve ongoing adaptation to long-term demands. We introduce the TPPCA in several domains of inquiry, which rely on fast adaptation processes (perceptual–cognitive–action coupling, performance routines, psychological crisis, reversal states), slow adaptation processes (i.e., career aspirations, burnout), and processes that can be either fast or slow (i.e., flow, affect and mood changes, emotion regulation).
Characterization of a Novel Murine Model of Staphylococcus saprophyticus Urinary Tract Infection Reveals Roles for Ssp and SdrI in Virulence

ABSTRACT Staphylococcus saprophyticus, an obligate human pathogen, is the most common Gram-positive causative agent of urinary tract infection (UTI) in young, healthy women. Despite the clinical importance of S. saprophyticus, little is known about how it causes disease in the urinary tract or how the host responds to the infection. Here we established an in vivo model to study both host and bacterial factors contributing to S. saprophyticus UTI. Using this model, we show that S. saprophyticus preferentially infects C3H/HeN murine kidneys instead of the bladder, a trait observed for multiple clinical isolates. Bacterial persistence in the kidneys was observed in C3H/HeN mice but not in C57BL/6 mice, indicating that host factors strongly contribute to the ability of S. saprophyticus to cause UTI. Using C3H/HeN mice as a model, histologic and immunofluorescence analyses of infected tissues revealed that S. saprophyticus induced epithelial cell shedding in the bladder and an inflammatory response characterized by macrophage and neutrophil infiltration in the bladder and kidneys. The inflammatory response correlated with increased production of proinflammatory cytokines and chemokines in both the bladder and the kidneys. Finally, we observed that the putative S. saprophyticus virulence factors Ssp and SdrI were important for persistence, but not for initial colonization, in the murine urinary tract. Thus, we characterized both host and bacterial factors involved in progression of S. saprophyticus UTI, and we describe a useful model system for studying factors involved in the pathogenesis of this Gram-positive uropathogen.
Question answering on interlinked data

The Data Web contains a wealth of knowledge on a large number of domains. Question answering over interlinked data sources is challenging due to two inherent characteristics. First, different datasets employ heterogeneous schemas and each one may only contain a part of the answer for a certain question. Second, constructing a federated formal query across different datasets requires exploiting links between the different datasets on both the schema and instance levels. We present a question answering system, which transforms user supplied queries (i.e. natural language sentences or keywords) into conjunctive SPARQL queries over a set of interlinked data sources. The contribution of this paper is two-fold: Firstly, we introduce a novel approach for determining the most suitable resources for a user-supplied query from different datasets (disambiguation). We employ a hidden Markov model, whose parameters were bootstrapped with different distribution functions. Secondly, we present a novel method for constructing a federated formal queries using the disambiguated resources and leveraging the linking structure of the underlying datasets. This approach essentially relies on a combination of domain and range inference as well as a link traversal method for constructing a connected graph which ultimately renders a corresponding SPARQL query. The results of our evaluation with three life-science datasets and 25 benchmark queries demonstrate the effectiveness of our approach.
The Three-dimensional Architecture of a Bacterial Genome and Its Alteration by Genetic Perturbation

SUMMARY We have determined the three-dimensional (3D) architecture of the Caulobacter crescentus genome by combining genome-wide chromatin interaction detection, live-cell imaging, and computational mod-eling. Using chromosome conformation capture carbon copy (5C), we derive $13 kb resolution 3D models of the Caulobacter genome. The resulting models illustrate that the genome is ellipsoidal with periodically arranged arms. The parS sites, a pair of short contiguous sequence elements known to be involved in chromosome segregation, are positioned at one pole, where they anchor the chromosome to the cell and contribute to the formation of a compact chromatin conformation. Repositioning these elements resulted in rotations of the chromosome that changed the subcellular positions of most genes. Such rotations did not lead to large-scale changes in gene expression, indicating that genome folding does not strongly affect gene regulation. Collectively, our data suggest that genome folding is globally dictated by the parS sites and chromosome segregation.
Photoreceptor‐specific expression, light‐dependent localization, and transcriptional targets of the zinc‐finger protein Yin Yang 1 in the chicken retina

The zinc‐finger transcription factor Yin Yang 1 (YY1) is a multifunctional protein that plays a critical role in embryonic development. Although it has been shown to play a role in eye development, its expression in the retina was not previously described. Here, we investigated YY1 expression in chicken tissues and we identified the neural retina as one of the tissues with highest YY1 protein levels. Immunohistochemical detection of YY1 in the retina revealed a clear‐cut photoreceptor specificity and day/night differences in the cytoplasmic localization of the protein. YY1 was also present at high concentration in the nuclei of some photoreceptors. Gel‐shift assays indicated YY1 bound to regulatory regions of several genes specifically expressed in photoreceptors. One of these genes, hydroxyindole‐O‐methyltransferase (EC 2.1.1.4), encodes the last enzyme of the melatonin synthesis pathway. Although over‐expression of chicken YY1 was not sufficient to activate the chicken hydroxyindole‐O‐methyltransferase promoter in HEK293 cells, the YY1‐binding site contained in this promoter was clearly required for full transcriptional activity in chicken embryonic retinal cells. These results suggest a role of YY1 in regulating the melatoninergic function of retinal photoreceptors.
The Ribosomal S10 Protein Is a General Target for Decreased Tigecycline Susceptibility

ABSTRACT Tigecycline is a translational inhibitor with efficacy against a wide range of pathogens. Using experimental evolution, we adapted Acinetobacter baumannii, Enterococcus faecium, Escherichia coli, and Staphylococcus aureus to growth in elevated tigecycline concentrations. At the end of adaptation, 35 out of 47 replicate populations had clones with a mutation in rpsJ, the gene that encodes the ribosomal S10 protein. To validate the role of mutations in rpsJ in conferring tigecycline resistance, we showed that mutation of rpsJ alone in Enterococcus faecalis was sufficient to increase the tigecycline MIC to the clinical breakpoint of 0.5 μg/ml. Importantly, we also report the first identification of rpsJ mutations associated with decreased tigecycline susceptibility in A. baumannii, E. coli, and S. aureus. The identified S10 mutations across both Gram-positive and -negative species cluster in the vertex of an extended loop that is located near the tigecycline-binding pocket within the 16S rRNA. These data indicate that S10 is a general target of tigecycline adaptation and a relevant marker for detecting reduced susceptibility in both Gram-positive and -negative pathogens.
An update and review of acute kidney injury in pediatrics

Objectives: To inform the pediatric intensivist of recent advancements in acute kidney injury diagnosis and management. Data Sources: Studies were identified from MEDLINE (OVID), PubMed, and the Cochrane Library for topics relevant to acute kidney injury. We also reviewed bibliographies of relevant studies. Data Extraction, Synthesis, and Outline Review: Because of the lack of prospective trials, a majority of information is extracted from observational and retrospective data. The pathophysiology section reviews acute kidney injury mechanisms and highlights data regarding distal injury from experimental acute kidney injury. The epidemiology section focuses on incidence and outcomes of acute kidney injury, highlighting new strategies for diagnosis. The management section cites studies investigating hemodynamic optimization, nutrition, and fluid management, including the indications and impact of continuous renal replacement therapy in fluid overload. Conclusions: There is limited data-driven evidence in pediatrics regarding effective therapy for acute kidney injury, a significant problem in the pediatric intensive care unit extending length of stay, ventilator days, and overall mortality. Sublethal kidney injury may be contributing to overall morbidity. We conclude that prospective clinical trials are needed to evaluate specific diagnostic aids, such as biomarkers, and therapeutic strategies, such as early initiation of continuous renal replacement therapy in children with fluid overload.
The importance of placebo effects in pain treatment and research.

OBJECTIVE To estimate the importance and implications of placebo effects in pain treatment and research from the existing literature, with emphasis on their magnitude and duration, the conditions influencing them, and proposed explanations. DATA SOURCES English-language articles and books identified through MEDLINE (1980 through 1993) and PsycLIT (1967 through 1993) database searching, bibliography review, and expert consultation. STUDY SELECTION Articles were included if they pertained to the review objectives. RESULTS Placebo response rates vary greatly and are frequently much higher than the often-cited one third. Placebos have time-effect curves, and peak, cumulative, and carryover effects similar to those of active medications. As with medication, surgery can produce substantial placebo effects, and this possibility is commonly overlooked in case series reports on back surgery. Individuals are not consistent in their placebo responses, and a placebo-responder personality has not been identified. Models advanced to explain placebo effects emphasize the role of anxiety, expectations, and learning. CONCLUSIONS Placebo effects influence patient outcomes after any treatment, including surgery, that the clinician and patient believe is effective. Placebo effects plus disease natural history and regression to the mean can result in high rates of good outcomes, which may be misattributed to specific treatment effects. The true causes of improvements in pain after treatment remain unknown in the absence of independently evaluated randomized controlled trials.
Representing Argumentation Frameworks in Answer Set Programming

This paper studies representation of argumentation frameworks (AFs) in answer set programming (ASP). Four different transformations from AFs to logic programs are provided under the complete semantics, stable semantics, grounded semantics and preferred semantics. The proposed transformations encode labelling-based argumentation semantics at the object level, and different semantics of AFs are uniformly characterized by stable models of transformed programs. We show how transformed programs can be used for solving AF problems such as query-answering, enforcement of arguments, and agreement of different AFs. The results exploit new connection between AF and logic programming, and enables one to realize AF on top of existing answer set solvers.
Turn customer input into innovation.

It's difficult to find a company these days that doesn't strive to be customer-driven. Too bad, then, that most companies go about the process of listening to customers all wrong--so wrong, in fact, that they undermine innovation and, ultimately, the bottom line. What usually happens is this: Companies ask their customers what they want. Customers offer solutions in the form of products or services. Companies then deliver these tangibles, and customers just don't buy. The reason is simple--customers aren't expert or informed enough to come up with solutions. That's what your R&D team is for. Rather, customers should be asked only for outcomes--what they want a new product or service to do for them. The form the solutions take should be up to you, and you alone. Using Cordis Corporation as an example, this article describes, in fine detail, a series of effective steps for capturing, analyzing, and utilizing customer input. First come indepth interviews, in which a moderator works with customers to deconstruct a process or activity in order to unearth "desired outcomes. " Addressing participants' comments one at a time, the moderator rephrases them to be both unambiguous and measurable. Once the interviews are complete, researchers then compile a comprehensive list of outcomes that participants rank in order of importance and degree to which they are satisfied by existing products. Finally, using a simple mathematical formula called the "opportunity calculation," researchers can learn the relative attractiveness of key opportunity areas. These data can be used to uncover opportunities for product development, to properly segment markets, and to conduct competitive analysis.
Analysis of Economic Determinants of Fertility in Iran: A Multilevel Approach

BACKGROUND During the last three decades, the Total Fertility Rate (TFR) in Iran has fallen considerably; from 6.5 per woman in 1983 to 1.89 in 2010. This paper analyzes the extent to which economic determinants at the micro and macro levels are associated with the number of children in Iranian households. METHODS Household data from the 2010 Household Expenditure and Income Survey (HEIS) is linked to provincial data from the 2010 Iran Multiple-Indicator Demographic and Health Survey (IrMIDHS), the National Census of Population and Housing conducted in 1986, 1996, 2006 and 2011, and the 1985-2010 Iran statistical year books. Fertility is measured as the number of children in each household. A random intercept multilevel Poisson regression function is specified based on a collective model of intra-household bargaining power to investigate potential determinants of the number of children in Iranian households. RESULTS Ceteris paribus (other things being equal), probability of having more children drops significantly as either real per capita educational expenditure or real total expenditure of each household increase. Both the low- and the high-income households show probabilities of having more children compared to the middle-income households. Living in provinces with either higher average amount of value added of manufacturing establishments or lower average rate of house rent is associated to higher probability of having larger number of children. Higher levels of gender gap indices, resulting in household's wife's limited power over household decision-making, positively affect the probability of having more children. CONCLUSION Economic determinants at the micro and macro levels, distribution of intra-household bargaining power between spouses and demographic covariates determined fertility behavior of Iranian households.
Premature Deaths: Russia's Radical Economic Transition in Soviet Perspective

THE 'WASHINGTON CONSENSUS', which for nearly a decade put the best face it could on Russia's mis-transition, is showing signs of crumbling.1 It is now acknowledged that the Russian Federation's post-communist depression was deep and painful, causing immense physical hardship and psychological stress. After reporting unem- ployment in the low single digits during the first half of the 1990s, it turns out that more than 17 million are seeking work or have left the labour force after years of discouragement.2 The time therefore has come for a dry-eyed assessment of whether acute privation during the 1990s caused a significant number of premature deaths. To mitigate the problem of ex post assumption fitting, detailed population projections prepared by the American Census Bureau in 1993 have been selected as the foundation for the null hypothesis that the physical hardships, social disruption and psychological distress associated with a 44% decline in Russia's GNP caused millions of premature deaths, in addition to any adverse impact they may have had on fertility. The exercise reveals that there were 3.4 million Russian premature deaths in 1990-98 plausibly attributable to the travails of post-communism.3 What went wrong? Why were policy makers so misguided? There are many possible explanations including bad advice from the Washington Consensus, but no full fledged mea culpas.4 This article tries to cut through the finger pointing by attributing Russia's latest bout of premature deaths to the penchant of post-tsarist political leaders like Lenin, Stalin, Khrushchev, Gorbachev and El'tsin for rash measures rather than carefully prepared reforms supported by the 'rule of law'. 5 There is no doubt that the Washington Consensus bears some responsibility for the victims of 'shock therapy'. Its nostrums influenced reformers in El'tsin's circle like Stanislav Shatalin, Grigorii Yavlinsky and Egor Gaidar, but key Western advisers like Anders Aslund and Jeffrey Sachs legitimately counter-claim that the Kremlin's reforms reflected the political agenda of the El'tsin administration, concerned more with destroying the vestiges of the Soviet state and building new institutions of cronyist power than establishing competitive free enterprise. It is in this sense that Russia's post-communist premature deaths are ascribed to the tradition of callous economic radicalism,6 rather than failed liberalisation. Russian leaders have repeatedly exhibited little self-restraint in eradicating their adversaries' economic institutions and must admit this vice if the cycle of premature deaths is to be broken.
How Geography Affects Quality

This paper connects the quality of product-level bilateral trade flows with the geographic position of the exporter. Theoretically we show that, in addition to commonly used importer characteristics, quality increases (i) in trade-weighted specific transportation cost to destinations other than the importer and (ii) in trade-weighted preference for quality of destinations other than the importer. These two channels extend the familiar Alchian–Allen and Linder theories to the multilateral setting.