Miracle-dz/UniFAR-FTUs huggingface dataset:
Scalable metagenomic taxonomy classification using a reference genome database

Motivation: Deep metagenomic sequencing of biological samples has the potential to recover otherwise difficult-to-detect microorganisms and accurately characterize biological samples with limited prior knowledge of sample contents. Existing metagenomic taxonomic classification algorithms, however, do not scale well to analyze large metagenomic datasets, and balancing classification accuracy with computational efficiency presents a fundamental challenge. Results: A method is presented to shift computational costs to an off-line computation by creating a taxonomy/genome index that supports scalable metagenomic classification. Scalable performance is demonstrated on real and simulated data to show accurate classification in the presence of novel organisms on samples that include viruses, prokaryotes, fungi and protists. Taxonomic classification of the previously published 150 giga-base Tyrolean Iceman dataset was found to take <20 h on a single node 40 core large memory machine and provide new insights on the metagenomic contents of the sample. Availability: Software was implemented in C++ and is freely available at http://sourceforge.net/projects/lmat Contact: allen99@llnl.gov Supplementary information: Supplementary data are available at Bioinformatics online.
Muscle activity in rat locomotion: Movement analysis and electromyography of the flexors and extensors of the elbow

Footfall patterns and time sequence of activity are described for white rats conditioned to run freely in an activity wheel (which they drive). Motion is described in terms of soft contact, hard contact, soft contact, and flip phases. Duration of stride decreases and length of stride increases from walk to trot to canter to gallop. Myographic analysis shows that the brachialis has a major tonic function after it fires strongly during the flip phase and during much of the hard contact phase. Animals running at canter or gallop show major asymmetries between forelimb muscles on the first paw and on the lead paw sides.
Dynamics of Forward and Backward Translocation of mRNA in the Ribosome

Translocation of the mRNA-tRNA complex in the ribosome, which is catalyzed by elongation factor EF-G, is one of critical steps in the elongation cycle of protein synthesis. Besides this conventional forward translocation, the backward translocation can also occur, which can be catalyzed by elongation factor LepA. However, the molecular mechanism of the translocation remains elusive. To understand the mechanism, here we study theoretically the dynamics of the forward translocation under various nucleotide states of EF-G and the backward translocation in the absence of and in the presence of LepA. We present a consistent explanation of spontaneous forward translocations in the absence of EF-G, the EF-G-catalyzed forward translocations in the presence of a non-hydrolysable GTP analogue and in the presence of GTP, and the spontaneous and LepA-catalyzed backward translocation. The theoretical results provide quantitative explanations of a lot of different, independent experimental data, and also provide testable predictions.
Development and Interpretation of New Sediment Rating Curve Considering the Effect of Vegetation Cover for Asian Basins

Suspended sediment concentration of a river can provide very important perspective on erosion or soil loss of one river basin ecosystem. The changes of land use and land cover, such as deforestation or afforestation, affect sediment yield process of a catchment through changing the hydrological cycle of the area. A sediment rating curve can describe the average relation between discharge and suspended sediment concentration for a certain location. However, the sediment load of a river is likely to be undersimulated from water discharge using least squares regression of log-transformed variables and the sediment rating curve does not consider temporal changes of vegetation cover. The Normalized Difference Vegetation Index (NDVI) can well be used to analyze the status of the vegetation cover well. Thus long time monthly NDVI data was used to detect vegetation change in the past 19 years in this study. Then monthly suspended sediment concentration and discharge from 1988 to 2006 in Laichau station were used to develop one new sediment rating curve and were validated in other Asian basins. The new sediment model can describe the relationship among sediment yield, streamflow, and vegetation cover, which can be the basis for soil conservation and sustainable ecosystem management.
The Role of Personality Traits in Young Adult Fruit and Vegetable Consumption

This project investigated how individual differences in the big-five personality traits (neuroticism, extraversion, openness to experience, conscientiousness, and agreeableness) predicted plant-food consumption in young adults. A total of 1073 participants from two samples of young adults aged 17–25 reported their daily servings of fruits, vegetables, and two unhealthy foods for comparison purposes using an Internet daily diary for 21 or 13 days (micro-longitudinal, correlational design). Participants also completed the Neuroticism, Extraversion, Openness Five Factor Inventory (NEO-FFI) measure of personality, and demographic covariates including gender, age, ethnicity, and body mass index (BMI). Analyses used hierarchical regression to predict average daily fruit and vegetable consumption as separate dependent variables from the demographic covariates (step 1) and the five personality traits (step 2). Results showed that young adults higher in openness and extraversion, and to some extent conscientiousness, ate more fruits and vegetables than their less open, less extraverted, and less conscientious peers. Neuroticism and agreeableness were unrelated to fruit and vegetable consumption. These associations were unique to eating fruit and vegetables and mostly did not extend to unhealthy foods tested. Young adult women also ate more fruit and vegetables than young adult men. Results suggest that traits associated with greater intellect, curiosity, and social engagement (openness and extraversion), and to a lesser extent, discipline (conscientiousness) are associated with greater plant-food consumption in this population. Findings reinforce the importance of personality in establishing healthy dietary habits in young adulthood that could translate into better health outcomes later in life.
Stem cells in gynaecology

Currently, there is enormous interest in stem cells as a new treatment modality for regenerative medicine, commencing when human embryonic stem (hES) cells were first cultured from spare in vitro fertilisation‐derived embryos. Emerging evidence also suggests that somatic stem cells may have greater differentiation potential. Stem cell research is now in an exciting phase of development and has the potential to dramatically influence therapeutics as hES cell derivatives and/or adult stem cells are applied to regenerative medicine or to deliver gene therapy. Human ES cells show apparently limitless proliferative potential and differentiation capacity into all tissue types. Adult stem cells are rare cells, which maintain the tissue in which they reside. The challenges facing the use of hES cells and adult stem cells in medicine are highlighted and examples of their use in laboratory studies and the clinic are given. Adult stem cells have been identified in diverse tissues, including human bone marrow, breast, prostate, brain and liver. We hypothesised that adult stem cells reside in the endometrium, a highly proliferative, cyclically regenerating tissue. Our research has demonstrated, for the first time, that human endometrium contains a small population of epithelial cells (0.22%) and stromal cells (1.25%) that exhibit stem/progenitor cell behaviour in vitro; clonogenicity. The progeny in these colonies have been characterised and growth factors supporting clonogenicity identified. The goal is to examine the role of putative endometrial stem/progenitor cells in proliferative disorders of human endometrium, such as endometriosis, adenomyosis, endometrial hyperplasia and endometrial cancer, and the action of hormone‐replacement therapy on the post‐menopausal endometrium.
The social, cultural and medicinal use of kava for twelve Tongan born men living in Auckland, New Zealand.

UNLABELLED Kava consumption is a very popular practise amongst Pacific people especially amongst the Tongan communities. The purpose of this paper is to identify some of the key cultural, social and medicinal elements of kava use amongst Tongan men. Twelve face to face interviews in this study were undertaken. The paper argues that kava drinking is strongly linked to many of the ceremonial, social and cultural obligations that are deeply embedded within the Tongan culture. The positive uses of kava include medicinal purposes, male bonding, alternative to alcohol consumption, reaffirming and establishing relationships amongst other Tongan men, The men also stated negative uses of kava such as it made them lazy, tired so they were not able to go to work, a lack of sexual activities by being too tired have sex with their partners, and very expensive to buy in New Zealand. AIM The aim of this paper is to discuss and examine the social, cultural and medicinal kava use amongst twelve Tongan born men living in Auckland, New Zealand. METHODS The study used qualitative methods, specifically individual interviews were conducted in Tongan or English. Participants were recruited through community networks in Auckland. A number of Tongan churches, Tongan medical clinics such as Langimailie, and kava clubs were approached to recruit participants. The open ended interview schedule covered themes such as access, quantity, frequency, and problems associated with kava use. The interviews were conducted by a Tongan researcher either in English or Tongan. All interviews were translated and transcribed into English. A thematic analysis based on multiple readings of the transcripts was used The analysis identified commonalities and differences. The study was granted ethical approval by the University of Auckland Human Subjects Ethics Committee in December 2004. Interviews were conducted at the beginning of 2005. Interviews were undertaken in a place where the participants felt comfortable. Interview times were arranged at a time convenient for the participants. All participants were given information sheets prior to interviews, and participants were asked to sign consent forms before the interviews commenced. These forms were provided in Tongan and English versions. Most of the interviews ranged between one to three hours. Interviews were audiotaped, and confidentiality was maintained throughout the research. PARTICIPANTS Twelve men were interviewed. All participants were Tongan men born and raised in Tonga. The ages of men ranged between 30 and 75 years. Most of the men had been residing in New Zealand for over 30 years, although some men had only been in New Zealand between 2-18 years. Most of the men were employed and a few had retired from work. Most of these men also belonged to a church. All of the men who participated were married.
Effects of the dietary protein content and the feeding level on protein and energy metabolism in Iberian pigs growing from 50 to 100 kg body weight.

Nutritional requirements of the Iberian pig, a slow-growing, obese porcine breed, are not well defined and seem to differ from those of conventional or high-performing pigs. The effects of the dietary protein content and the feeding level on the utilisation of metabolisable energy (ME) and the rates of gain, protein, and fat deposition were studied with 81 Iberian castrates growing from 50 to 100 kg body weight (BW) by using the comparative slaughter technique. The animals were fed 4 diets providing 145, 120, 95, and 70 g ideal crude protein (CP) per kg dry matter (DM), and containing 13.94, 14.29, 14.56, and 14.83 MJ ME per kg DM, respectively. Three levels of feeding were evaluated: 0.60, 0.80, and 0.95 × ad libitum intake. Growth rate increased (linear and quadratic, P < 0.001) as the dietary ideal CP content decreased. It also increased with the feeding level (linear, P < 0.001; quadratic, P < 0.05). Gain:feed and gain:ME intake improved by decreasing the ideal CP content in the diet (linear, P < 0.001 and P < 0.05, respectively; quadratic P < 0.001 for both variables). Increasing the feeding level improved linearly gain:feed and gain:ME intake ( P < 0.001). Protein deposition (PD):ME intake ranged between 1.23 and 1.44 g/MJ, and it showed a tendency to reach the maximum value when the diet providing 95 g ideal CP per kg DM was fed (quadratic, P = 0.078). When this diet was offered at 0.95 × ad libitum, PD reached a maximum value of 71 g/day. This dietary treatment resulted in average values for average daily gain and retained energy (RE) of 854 g/day and 21.4 MJ/day, respectively. The average rate of gain was 19.93 g/MJ increase in ME intake, equivalent to an energy cost of 50.2 kJ ME per g gain, irrespective of the dietary ideal CP content. Also, the overall marginal efficiency of protein deposition (ΔPD:ΔME; g/MJ) was 1.34. Increasing the feeding level led to increases in PD (linear, P < 0.001) and RE (linear, P < 0.001; quadratic, P < 0.01) irrespective of the dietary ideal CP concentrations. Between 50 and 100 kg BW, the chemical composition of 1 kg gain averaged 78, 592, 28.7, and 284 g for CP, fat, ash, and water respectively. The net efficiency of use of ME for growth ( kg) and the maintenance energy requirements were 0.606 and 396 kJ/kg BW 0.75 per day, respectively. The results support earlier findings that the genotype has marked effects on protein and energy metabolism of growing pigs and underline important compositional differences of the Iberian pig compared with conventional or modern porcine genotypes.
Conducting Curriculum-Based Measurement with Computerized Data Collection: Effects on Efficiency and Teacher Satisfaction

This study assessed the efficiency of and teacher satisfaction with curriculum-based measurement (CBM) when student performance data are collected by teachers or by computers. Participants were 20 special education teachers, randomly assigned to teacher and computer administration groups. Each practitioner selected two mildly handicapped pupils for participation. For 15 weeks, teachers employed CBM in reading, spelling, and math, with data collected by teachers or by computers. Ten weeks into the study, teachers and students were observed during measurement and evaluation activities, and durations of time allocated to CBM procedures were recorded. Teacher satisfaction was indexed with a questionnaire at the study's completion. Observational data indicated that teachers spent less time in measurement and evaluation when data were collected by computers; further, satisfaction data revealed that computer-data-collection teachers were more satisfied with the procedures. However, students spent more time in measurement with computer data collection. Implications for special education practice are discussed.
Platoon-based cyclists cooperative system

Bicycle use has steadily risen its share of total urban traffic over the last decade. This has been the result of city governments promotion of alternative forms of transportation, in the search for finding strategies that help reduce traffic congestion. Although benefits of cycling in congestion and pollution are concrete, in several cities the increment of cyclists has gotten to the point to overflow the infrastructure, deriving in safety risks and gridlocks due to the lack of explicit coordination among cyclists. This paper presents the integration of two strategies that so far have been considered completely independent: cooperative driving and cycling. Our project addresses the coordination of collective behavior of platoons of cyclists that could pervade dedicated express roads such as the London's 18 mile East-West Cycle Superhighway. The proposed platoon-based cyclists cooperative system can be defined as a networked cyber-physical system with an additional challenge related to the human factor. Different from traditional automated platooning, in the proposed system cyclists respond to a Cooperative Adaptive Cruise Control delivered through specific human-machine interfaces (HMI) designed to elicit the expected response from cyclists. A smart bicycle has been implemented to validate the accuracy of the proposed HMI, and simulations of the complete system are provided to determine the impact of the human error factor in the effectiveness of the cooperative cycling system.
Cell culture propagation of a coronavirus isolated from cows with winter dysentery

Fecal filtrates from cows with winter dysentery were inoculated into gnotobiotic and conventional calves, and a coronavirus was isolated from calf feces. Cytopathic effects were observed on human rectal tumor cells but not bovine cell cultures. The winter dysentery isolates morphologically and antigenically resembled the Mebus strain of bovine coronavirus.
Dynamic interactions between splicing snRNPs, coiled bodies and nucleoli revealed using snRNP protein fusions to the green fluorescent protein.

The U1, U2, U4/U6, and U5 small nuclear ribonucleoproteins (snRNPs) are subunits of splicing complexes that remove introns from mRNA precursors. snRNPs show a complex, transcription-dependent localization pattern in the nucleoplasm of mammalian cells that results from their association with several distinct subnuclear structures, including interchromatin granule clusters, perichromatin fibrils, and coiled bodies. Here we report the analysis of snRNP localization and interaction with the coiled body in live human cells using fusions of snRNP proteins and p80 coilin to the Green Fluorescent Protein (GFP). Despite the large size of the GFP tag, GFP fusions to both the core snRNP SmE and U1 specific U1A proteins assemble into snRNP particles and give an identical nuclear localization pattern to their endogenous counterparts. GFP-coilin localizes specifically to coiled bodies in a transcription-dependent fashion and provides an accurate marker for coiled bodies in a variety of human cell lines. Treatment of cells with the selective ser/thr-protein phosphatase inhibitor, okadaic acid, causes both GFP-snRNP and GFP-coilin proteins to accumulate within nucleoli, but does not result in nucleolar accumulation of the GFP-fused non-snRNP protein splicing factor ASF/SF2. In all four human cell lines tested, expression of a GFP-fused p80 coilin mutant with a single serine to aspartate substitution also caused nucleolar accumulation of splicing snRNPs and coilin, but not ASF/SF2, in structures resembling coiled bodies when viewed by electron microscopy. This work establishes an experimental system for analyzing snRNP trafficking in living cells and provides evidence that a reversible protein phosphorylation mechanism is involved in regulating interaction of snRNPs and coiled bodies with the nucleolus.
Medial Patellofemoral Ligament Reconstruction

Background: Medial patellofemoral ligament (MPFL) reconstruction is a routine procedure for patellar instability. The majority of the techniques require hardware fixation or a bony procedure at the patella. However, most of the complications described in the literature can be attributed to patellar fixation. The “superficial quad technique” uses the superficial slip of the quadriceps tendon as the graft material, which provides a better anatomic match to the native MPFL. Hypothesis: The superficial quad technique provides anatomic patellar fixation without a bony procedure and without patellar complications. Study Design: Case series; Level of evidence, 4. Methods: The study included 32 patients (10 male, 22 female; mean age, 25 years) who underwent MPFL reconstruction using the superficial quad technique and who were followed for a mean duration of 38 months. Objective assessment was performed and Kujala scores were obtained preoperatively and at the time of final follow-up. Results: There were no patellar complications, including redislocation, in the present study. The mean Kujala score improved to 91.25 (range, 73-100) from a preoperative score of 49.31 (range, 23-62). Conclusion: The results were comparable with those of other studies in the literature that used hamstring grafts, but without associated patellar complications. The superficial quad technique uses graft material that is a better anatomic match to the native MPFL. It provides anatomic patellar fixation without a bony procedure.
Primitive Classification and Postmodernity: Towards a Sociological Notion of Fiction

Introduction: Sociology beyond Modernism Postmodernist thinking in sociology is easily dismissed as gibberish taken over from French intellectuals and literary critics surveying the world from their Parisian desks or, worse still, from the vantage point of their brief travels to La Californie. It can be seen as an ephemeral fashion taken up by social theorists who are out of ideas, theorists who are finally getting bored with reinterpreting Weber, Durkheim and Marx. ) But it can also be seen as a movement sustained by developments within sociology which imply a rupture with Enlightenment thinking, a negation of many of the definitive features which have been associated with the modern. These developments nourish a break with modernist claims by offering empirical documentation for their findings, a feature not entirely irrelevant to a science that wants to make assertions about the social world. In addition, they suggest that postmodernity is something more than a chapter in the sociology of intellectuals and their malaise with the world, as Bauman suggests (1988), or a trend in aestheticism keyed to increased individualism, multiple choices, and 'self-enrichment' or 'self-enlargement' (Rorty, 1986). The perspectives which push sociology from within beyond the grand master themes of modernist thinking and modernist research, differentiation and rationalization, and which lead, as one might say, to pastmodern thinking, are microanalysis and construc­ tionism. Microanalysis is the detailed description of social episodes through means such as ethnography, discourse analysis or visual methods. It has flourished in ethnomethodology, symbolic inter­ actionism, social phenomenology, and so on, and has documented in detail the existence of life-worlds which theorists such as Habermas (1983) think we have lost, and the relevance of the body,
Characterization of Genetic Diversity of Carbapenem-Resistant Acinetobacter baumannii Clinical Strains Collected from 2004 to 2007

ABSTRACT Genotypes of carbapenem-resistant Acinetobacter baumannii collected by the clinical microbiology laboratory of a university hospital in Chicago, IL, between 2004 and 2007 were analyzed by pulsed-field gel electrophoresis. A single genotype established predominance after being introduced in 2005. Analysis of carbapenemases by PCR revealed that imipenem resistance but not meropenem resistance was associated with the presence of blaOXA-23 and blaOXA-40 genes.