Miracle-dz/UniFAR-FTUs huggingface dataset:
Accuracy and efficiency of algorithms for the demarcation of bacterial ecotypes from DNA sequence data

Identification of closely related, ecologically distinct populations of bacteria would benefit microbiologists working in many fields including systematics, epidemiology and biotechnology. Several laboratories have recently developed algorithms aimed at demarcating such 'ecotypes'. We examine the ability of four of these algorithms to correctly identify ecotypes from sequence data. We tested the algorithms on synthetic sequences, with known history and habitat associations, generated under the stable ecotype model and on data from Bacillus strains isolated from Death Valley where previous work has confirmed the existence of multiple ecotypes. We found that one of the algorithms (ecotype simulation) performs significantly better than the others (AdaptML, GMYC, BAPS) in both instances. Unfortunately, it was also shown to be the least efficient of the four. While ecotype simulation is the most accurate, it is by a large margin the slowest of the algorithms tested. Attempts at improving its efficiency are underway.
Pathophysiology of reverse cholesterol transport. Insights from inherited disorders of lipoprotein metabolism.

O n the basis of its kinetic behavior, the total cholesterol of body tissues can be divided into three major pools, which differ in their mean rates of exchange with plasma cholesterol. Each pool can be expanded by addition of endogenously synthesized cholesterol, cholesterol from the diet, or both. The only route of excretion of quantitative significance is via the hepato-biliary system, as cholesterol itself and as bile acids. Although endogenous synthesis is under feedback control, it cannot be completely suppressed; on the average, a minimum of about 20 mg is produced per kilogram of body weight per day. As cholesterol absorption by the jejunum is not actively regulated, the maintenance of a near-constant body content of cholesterol must be largely dependent on the efficiency of its elimination via the liver.
A Cost Effective sensorless vector control of 4- Switch 3-Phase Inverter Fed IM using MRAS

This paper investigates performance of a Model reference adaptive system (MRAS) based cost-effective drive system of an induction motor (IM) for low-cost applications. In this paper, the MRAS is used as a speed estimator and the motor is fed from a four-switch three-phase (FSTP) inverter instead of a conventional six-switch three-phase (SSTP) inverter. This configuration reduces the cost of the inverter, the switching losses, and the complexity of the control algorithms. The robustness of the proposed MRAS-based FSTP inverter fed IM drive is verified by Experimental results at different operating conditions. A comparison of the proposed FSTP inverter fed IM drive with a conventional SSTP inverter system is also made in terms of the performance analysis. The proposed FSTP inverter fed IM drive is found quite acceptable considering its performance, cost reduction and other advantages. DOI: http://dx.doi. org/10.11591/ijpeds.v1i2. 100
Inhibition of Endoplasmic Reticulum-Associated Degradation in CHO Cells Resistant to Cholera Toxin, Pseudomonas aeruginosa Exotoxin A, and Ricin

ABSTRACT Many plant and bacterial toxins act upon cytosolic targets and must therefore penetrate a membrane barrier to function. One such class of toxins enters the cytosol after delivery to the endoplasmic reticulum (ER). These proteins, which include cholera toxin (CT), Pseudomonas aeruginosa exotoxin A (ETA), and ricin, move from the plasma membrane to the endosomes, pass through the Golgi apparatus, and travel to the ER. Translocation from the ER to the cytosol is hypothesized to involve the ER-associated degradation (ERAD) pathway. We developed a genetic strategy to assess the role of mammalian ERAD in toxin translocation. Populations of CHO cells were mutagenized and grown in the presence of two lethal toxins, ETA and ricin. Since these toxins bind to different surface receptors and attack distinct cytoplasmic targets, simultaneous acquisition of resistance to both would likely result from the disruption of a shared trafficking or translocation mechanism. Ten ETA- and ricin-resistant cell lines that displayed unselected resistance to CT and continued sensitivity to diphtheria toxin, which enters the cytosol directly from acidified endosomes, were screened for abnormalities in the processing of a known ERAD substrate, the Z form of α1-antitrypsin (α1AT-Z). Compared to the parental CHO cells, the rate of α1AT-Z degradation was decreased in two independent mutant cell lines. Both of these cell lines also exhibited, in comparison to the parental cells, decreased translocation and degradation of a recombinant CTA1 polypeptide. These findings demonstrated that decreased ERAD function was associated with increased cellular resistance to ER-translocating protein toxins in two independently derived mutant CHO cell lines.
The Steady-State Pharmacokinetics of Nelfinavir in Combination with Tenofovir in HIV-Infected Patients

Background The nucleotide analogue, tenofovir, has been shown to lower plasma atazanavir levels in pharmacokinetic trials, an interaction that may be partly reversed by the addition of ritonavir, whereas plasma tenofovir levels are themselves raised when the drug is combined with lopinavir/ritonavir. Objective To investigate the effect of tenofovir coadministration on the steady-state pharmacokinetics of nelfinavir in HIV-infected patients. Methods Eighteen patients received nelfinavir 1250 mg twice daily plus prescribed nucleoside reverse transcriptase inhibitors for at least 14 days, with pharmacokinetic measurements performed on day 15. Treatment with nelfinavir was continued for another 7 days with the addition of 300 mg tenofovir once daily. Pharmacokinetic measurements were repeated on day 22. Plasma samples were analysed by liquid chromatography–tandem mass spectrometry for nelfinavir, its primary metabolite, M8, and tenofovir. The parameters AUC0–12, C0, Cmax and Tmax were compared for nelfinavir with and without tenofovir by calculating geometric mean ratios (GMRs) of the pharmacokinetic parameters with associated 95% confidence intervals (95% CIs). Safety was assessed throughout the study. Results The addition of tenofovir to the nelfinavir-based regimen had no effect on the pharmacokinetics of nelfinavir. The GMR of the nelfinavir AUC0–12 values was 0.97 (95% CI: 0.80–1.17). There was a slight decrease in M8 metabolite (AUC0–12 ratio, 0.87; 95% CI: 0.68–1.11) but this was not significant. No serious adverse events occurred through the study period. Conclusion Nelfinavir does not require dose adjustment when coadministered with tenofovir and appears to be well-tolerated by HIV-infected patients.
Feature-dependent compensation in speech recognition

Several mismatch conditions can be modeled as an additive bias. This bias is considered independent of the observation vectors, although this approximation is not always accurate. In this paper the dependence of the bias on the observation vectors is taken into consideration in the context of compensating the GSM coding distortion in speech recognition. However, the results presented here can easily be generalized to deal with other types of mismatch. The coding-decoding distortion is modeled here as feature-dependent. This model is employed to propose an ExpectationMaximization (EM) estimation algorithm of the codingdecoding distortion that is able to cancel the effect of GSM coder with as few as one adapting utterance. Finally, the feature-dependent adaptation can give word error rate (WER) 26% lower than the featureindependent model.
Kynurenines in CNS disease: regulation by inflammatory cytokines

The kynurenine pathway (KP) metabolizes the essential amino acid tryptophan and generates a number of neuroactive metabolites collectively called the kynurenines. Segregated into at least two distinct branches, often termed the “neurotoxic” and “neuroprotective” arms of the KP, they are regulated by the two enzymes kynurenine 3-monooxygenase and kynurenine aminotransferase, respectively. Interestingly, several enzymes in the pathway are under tight control of inflammatory mediators. Recent years have seen a tremendous increase in our understanding of neuroinflammation in CNS disease. This review will focus on the regulation of the KP by inflammatory mediators as it pertains to neurodegenerative and psychiatric disorders.
Estimates of lateral and longitudinal bond energies within the microtubule lattice

We developed a stochastic model of microtubule (MT) assembly dynamics that estimates tubulin–tubulin bond energies, mechanical energy stored in the lattice dimers, and the size of the tubulin-GTP cap at MT tips. First, a simple assembly/disassembly state model was used to screen possible combinations of lateral bond energy (ΔGLat) and longitudinal bond energy (ΔGLong) plus the free energy of immobilizing a dimer in the MT lattice (ΔGS) for rates of MT growth and shortening measured experimentally. This analysis predicts ΔGLat in the range of −3.2 to −5.7 kBT and ΔGLong plus ΔGS in the range of −6.8 to −9.4 kBT. Based on these estimates, the energy of conformational stress for a single tubulin-GDP dimer in the lattice is 2.1–2.5 kBT. Second, we studied how tubulin-GTP cap size fluctuates with different hydrolysis rules and show that a mechanism of directly coupling subunit addition to hydrolysis fails to support MT growth, whereas a finite hydrolysis rate allows growth. By adding rules to mimic the mechanical constraints present at the MT tip, the model generates tubulin-GTP caps similar in size to experimental estimates. Finally, by combining assembly/disassembly and cap dynamics, we generate MT dynamic instability with rates and transition frequencies similar to those measured experimentally. Our model serves as a platform to examine GTP-cap dynamics and allows predictions of how MT-associated proteins and other effectors alter the energetics of MT assembly.
Multi-User Medium Access Control in Wireless Local Area Network

We propose a multi-user medium access control (MAC) protocol to simultaneously support multi-packet transmission (MPT) and multi-packet reception (MPR) in wireless local area networks. By assuming perfect physical layer functions, we evaluate the maximum number of active stations that can be supported under different traffic arrival rates. Our analysis show that when the number of transmitting antennas is K=2, simultaneous MPT and MPR supports 40~50% more stations than previous multi-user MAC that uses only MPT. The gain increases to 60% when short packets (40 bytes) are used. When K=4, the advantage of MPT+MPR over MPT-only enlarges to 130%. We also investigated the impacts of imperfect physical layer functions and the effects of enabling or disabling RTS/CTS in uplink.
Modifications and Accommodations Medford Middle School Teachers Make For Students Demonstrating Behaviors Of Attention Deficit / Hyperactivity Disorder

Strick Jacqueline M. (Writer) (Last Name) (First) (Initial) Modifications and Accommodations Medford Middle School Teachers Make For ______ (Title) Students Demonstrating Behaviors of Attention Deficit/Hyperactivity Disorder (AD/HD). K-12 School Guidance & Counseling Amy Schlieve 12/2000 ___49_______ (Graduate Major) (Research Advisor) (Month/Year) ( Pg.) APA (Name of Style Manual Used in this Study) This study involves Medford Middle School teachers identifying the modifications and/or accommodations they make for children that demonstrate Attention Deficit / Hyperactivity Disorder (AD/HD) type behaviors in the classroom setting. The teachers surveyed encompass all subjects including the Related Arts classes of band, chorus, physical education, art and family and consumer education. The six behaviors identified in the survey were taken from the DSMIV criteria for diagnosing AD/HD in children. Part one of each question was the identified behavior and how the teacher accommodated it. Part two of the behavioral question was a continuum of the level of tolerance the teacher has for each specific behavior. The continuum range from “Little Tolerance” (1) to “Some Tolerance” (3) to “Much Tolerance” (5). In addition to the six behavioral questions, the teachers were asked to respond as to what their definition of a
Can Ontologies Improve Web Search Engine Effectiveness Before the Advent of the Semantic Web?

The advent of the semantic web will not be immediate, due to a shortage of knowledge engineering manpower to annotate a critical mass of web documents with concepts from ontologies. In this paper, we argue that widecoverage linguistic ontologies have an alternative usage to improve web search effectiveness while the web remains predominantly textual. They can be used by search engines to perform simple semantic processing, such as automatically expanding the query keywords with alternate wordings of the same or immediately neighboring concepts. We present a conclusive empirical experiment that shows that sizable relative effectiveness gains can be achieved by various expansion strategies for both unbounded and bounded retrieval result sets. This experiment also shows that the effectiveness of such ontology-boosted search on a textual web with no semantic annotations remains far away from the very high precision and recall promise of the semantic web.
Effects of Computer-assisted Cognitive Rehabilitation Training on the Cognition and Static Balance of the Elderly

[Purpose] The purpose of this study was to investigate the effects of a six-week-long computer-assisted cognitive rehabilitation training program on the improvement of cognition and balance abilities of the elderly. [Subjects] Thirty healthy elderly people, aged 65 to 80, were randomly assigned either to the training group (n=15) or the control group (n=15). [Methods] Cognitive functions were evaluated using MMSE-K, and the BioRescue AP 153 (RMINGENIERIE, France) was used to examine subjects’ changes in static balance. [Results] The MMSE-K score showed a significant change over the course of the treatment period in the training group, but not in the control group. The sway area and sway path length decreased significantly in the training group, but it did not show any changes in the control group. [Conclusion] Computer-assisted cognitive rehabilitation training is an effective intervention method for the improvement of the cognition and balance abilities of the elderly.
The influence of social desirability as a response set on the measurement of values/preferences related to work

Abstract The deleterious effects of social desirability response sets on the interpretation of psychological test scores has been a field of investigation by psychologists for some decades. However, in the specific context of measuring values/preferences related to work, most test constructors and researchers appear willing to accept Super's (1973) view that social desirability is not a major problem. Tbe empirical basis for such a statement is principally a study by Super and Mowry (1962) which is open to a number of methodological criticism. This paper reports research intended to provide more information about the relationship between social desirability and value/preference test scores. In Study 1, previous data gathered for the Work Aspect Preference Scale (Pryor, 1981a) on senior high school students was reanalysed by comparing the respective “social desirability” scales of tbe Sixteen Personality Factor Questionnaire, Eysenck Personality Inventory and the Vocational Preference Inventory with the su.
TET2 as an epigenetic master regulator for normal and malignant hematopoiesis

DNA methylation is one of the critical epigenetic modifications regulating various cellular processes such as differentiation or proliferation, and its dysregulation leads to disordered stem cell function or cellular transformation. The ten‐eleven translocation (TET) gene family, initially found as a chromosomal translocation partner in leukemia, turned out to be a key enzyme for DNA demethylation. TET genes hydroxylate 5‐methylcytosine to 5‐hydroxymethylcytosine, which is then converted to unmodified cytosine through multiple mechanisms. Somatic mutations of the TET2 gene were reported in a variety of human hematological malignancies such as leukemia, myelodysplastic syndrome, and malignant lymphoma, suggesting a critical role for TET2 in hematopoiesis. The importance of the TET‐mediated cytosine demethylation pathway is also underscored by a recurrent mutation of isocitrate dehydrogenase 1 (IDH1) and IDH2 in hematological malignancies, whose mutation inhibits TET function through a novel oncometabolite, 2‐hydroxyglutarate. Studies using mouse models revealed that TET2 is critical for the function of hematopoietic stem cells, and disruption of TET2 results in the expansion of multipotent as well as myeloid progenitors, leading to the accumulation of premalignant clones. In addition to cytosine demethylation, TET proteins are involved in chromatin modifications and other cellular processes through the interaction with O‐linked β‐N‐acetylglucosamine transferase. In summary, TET2 is a critical regulator for hematopoietic stem cell homeostasis whose functional impairment leads to hematological malignancies. Future studies will uncover the whole picture of epigenetic and signaling networks wired with TET2, which will help to develop ways to intervene in cellular pathways dysregulated by TET2 mutations.
Bone Marrow Stem Cells Do Not Contribute to Endometrial Cell Lineages in Chimeric Mouse Models

Studies from five independent laboratories conclude that bone marrow stem cells transdifferentiate into endometrial stroma, epithelium, and endothelium. We investigated the nature of bone marrow‐derived cells in the mouse endometrium by reconstituting irradiated wild type recipients with bone marrow containing transgenic mTert‐green fluorescent protein (GFP) or chicken β‐actin (Ch β‐actin)‐GFP reporters. mTert‐GFP is a telomerase marker identifying hematopoietic stem cells and subpopulations of epithelial, endothelial, and immune cells in the endometrium. Ch β‐actin‐GFP is a ubiquitous reporter previously used to identify bone marrow‐derived cells in the endometrium. Confocal fluorescence microscopy for GFP and markers of endometrial and immune cells were used to characterize bone marrow‐derived cells in the endometrium of transplant recipients. No evidence of GFP+ bone marrow‐derived stroma, epithelium, or endothelium was observed in the endometrium of mTert‐GFP or Ch β‐actin‐GFP recipients. All GFP+ cells detected in the endometrium were immune cells expressing the pan leukocyte marker CD45, including CD3+ T cells and F4/80+ macrophages. Further examination of the Ch β‐actin‐GFP transplant model revealed that bone marrow‐derived F4/80+ macrophages immunostained weakly for CD45. These macrophages were abundant in the stroma, infiltrated the epithelial and vascular compartments, and could easily be mistaken for bone marrow‐derived endometrial cells. We conclude that it is unlikely that bone marrow cells are able to transdifferentiate into endometrial stroma, epithelium, and endothelium. This result has important therapeutic implications, as the expectation that bone marrow stem cells contribute directly to endometrial regeneration is shaping strategies designed to regenerate endometrium in Asherman's syndrome and to control aberrant endometrial growth in endometriosis. Stem Cells 2018;36:91–102
Barriers to disseminating brief CBT for voices from a lived experience and clinician perspective

Access to psychological therapies continues to be poor for people experiencing psychosis. To address this problem, researchers are developing brief interventions that address the specific symptoms associated with psychosis, i.e., hearing voices. As part of the development work for a brief Cognitive Behaviour Therapy (CBT) intervention for voices we collected qualitative data from people who hear voices (study 1) and clinicians (study 2) on the potential barriers and facilitators to implementation and engagement. Thematic analysis of the responses from both groups revealed a number of anticipated barriers to implementation and engagement. Both groups believed the presenting problem (voices and psychosis symptoms) may impede engagement. Furthermore clinicians identified a lack of resources to be a barrier to implementation. The only facilitator to engagement was reported by people who hear voices who believed a compassionate, experienced and trustworthy therapist would promote engagement. The results are discussed in relation to how these barriers could be addressed in the context of a brief intervention using CBT techniques.
Ethnobotany of Kuta (Eleocharis sphacelata) in Bay of Plenty and Northland, New Zealand

Kuta or paopao (Eleocharis sphacelata) is a wetland plant of Maori cultural significance. It has special weaving qualities and is a biologically significant member of the wetland ecological community. Published information, and interviews with weavers and historians concerning traditional knowledge and practices pertaining to kuta is reported and discussed. Kuta's indigenous whakapapa is seen to reflect its biological genealogy.
NIVELES DE ACTIVIDAD FÍSICA EN ESTUDIANTES UNIVERSITARIOS: DIFERENCIAS EN FUNCIÓN DEL GÉNERO, LA EDAD Y LOS ESTADOS DE CAMBIO

The objective was to analyze the levels of moderate to vigorous physical activity (MVPA) in university students. Likewise, it was analyzed PA levels by gender, age and state of change of the Transtheoretical Model. 901 students, 408 men and 493 women, completed the IPAQ-SF and a question to evaluate the stages of change. Among the results, it highlights that 51.39% of students do not achieve the international recommendations of 30 minutes of MVPA practice per day, with a higher compliance in men. Regarding the states of change, in terms of levels of MVPA is concerned, significantly higher values were seen in the action stage and maintenance stage, compared to other stages of change. This suggests intervention guidelines for the development of intervention programs that affect the promotion of PA in the university stage.
Simulation infrastructure for the next kilo-x 86-64 Chips

The enhancement in silicon technology facilitates the integration of a higher number of cores on a single chip. Considering the current CMOS integration technology tendency; in the next future, systems are expected to scale up the number of cores, resulting in architectures composed by thousands of cores (i.e., namely kilocore architecture). The architecture of these kilo-core systems is still an open issue (i.e., number and type of cores, number of levels in the cache memory hierarchy, usage of specialized accelerators, interconnections types, etc.). The simulators provides high benefit in finding out architectural designs trade-offs for such next generation systems. This paper proposes a simulation framework based on the COTSon infrastructure, able to create thousands of virtual x86-64 cores. The framework offers a full-system architectural simulator and a well balanced trade-off between simulation speed and accuracy. Experimental outcomes demonstrates for our framework the possibility correctly simulate a large many-core machine.