Miracle-dz/UniFAR-FTUs huggingface dataset:
Enhancing Terpene Yield from Sugars via Novel Routes to 1-Deoxy-d-Xylulose 5-Phosphate

ABSTRACT Terpene synthesis in the majority of bacterial species, together with plant plastids, takes place via the 1-deoxy-d-xylulose 5-phosphate (DXP) pathway. The first step of this pathway involves the condensation of pyruvate and glyceraldehyde 3-phosphate by DXP synthase (Dxs), with one-sixth of the carbon lost as CO2. A hypothetical novel route from a pentose phosphate to DXP (nDXP) could enable a more direct pathway from C5 sugars to terpenes and also circumvent regulatory mechanisms that control Dxs, but there is no enzyme known that can convert a sugar into its 1-deoxy equivalent. Employing a selection for complementation of a dxs deletion in Escherichia coli grown on xylose as the sole carbon source, we uncovered two candidate nDXP genes. Complementation was achieved either via overexpression of the wild-type E. coli yajO gene, annotated as a putative xylose reductase, or via various mutations in the native ribB gene. In vitro analysis performed with purified YajO and mutant RibB proteins revealed that DXP was synthesized in both cases from ribulose 5-phosphate (Ru5P). We demonstrate the utility of these genes for microbial terpene biosynthesis by engineering the DXP pathway in E. coli for production of the sesquiterpene bisabolene, a candidate biodiesel. To further improve flux into the pathway from Ru5P, nDXP enzymes were expressed as fusions to DXP reductase (Dxr), the second enzyme in the DXP pathway. Expression of a Dxr-RibB(G108S) fusion improved bisabolene titers more than 4-fold and alleviated accumulation of intracellular DXP.
Food Intake Activity Detection Using a Wearable Microphone System

A method for non-invasive monitoring of human food intake behavior and long-term dietary protocol has been developed by the sole use of chewing and swallowing sound sensors. A novel sensor system has been built containing an in-ear microphone and a reference microphone integrated in a hearing aid case in order to record chewing and swallowing sounds in the ear canal and environmental noise, respectively. Using manual labeled records of the food intake sounds of 40 participants we developed an algorithm to detect food intake activity in sound data. Comparison between sounds from both microphones enables the discrimination between internal and external sounds.
A hairpin structure upstream of the terminator hairpin required for ribosomal protein L4-mediated attenuation control of the S10 operon of Escherichia coli

Ribosomal protein L4 of Escherichia coli regulates transcription of the 11-gene S1O operon by promoting premature termination of transcription (attenuation) at a specific site within the 172-base untranslated leader. We have analyzed the roles of various domains of the leader RNA in this transcription control. Our results indicate that the first 60 bases of the leader, forming the three proximal hairpin structures, are not essential for in vivo L4-mediated attenuation control. However, a deletion removing the fourth hairpin, which is immediately upstream of the terminator hairpin, eliminates L4's effect on transcription. Base changes disrupting complementarity in the 6-bp stem of this hairpin also abolish L4 control, but compensatory base changes that restore complementarity also restore L4's effect. In vitro transcription studies confirm that this hairpin structure is necessary for L4's role in stimulating transcription termination by RNA polymerase.
DIAGNOSTIC PERFORMANCE OF WAIST CIRCUMFERENCE MEASUREMENTS FOR PREDICTING CARDIOMETABOLIC RISK IN MEXICAN CHILDREN.

OBJECTIVE The accumulation of abdominal fat is associated with cardiometabolic abnormalities. Waist circumference (WC) measurements allow an indirect evaluation of abdominal adiposity. However, controversy exists over which WC reference values are the most suitable for identifying the pediatric population at risk. The aim of the study was to evaluate the ability of various WC indices to identify abdominal obesity as diagnostic tools for predicting cardiometabolic risk in Mexican children and adolescents. METHODS Anthropometric measurements were performed and biochemical profiles determined in a crosssectional study that included 366 children and adolescents. Four parameters were used to evaluate abdominal obesity in our study group: (1) WC >90th percentile, according to the Fernández reference in a Mexican-American population measured by the National Center for Health Statistics (NCHS) technique; (2) WC >90th percentile, according to the Klünder reference in a Mexican population (measured by the World Health Organization [WHO] technique); (3) waist-to-height ratio (WHtR) >0.5 according to WHO; and (4) WHtR >0.5 according to NCHS. The ability of each of the indices to discriminate cardiometabolic abnormalities (fasting plasma glucose, dyslipidemia, and hypertension) was assessed. RESULTS WHtR >0.5 according to WHO or NCHS references showed greater sensitivity to detect metabolic abnormalities compared to percentile reference parameters (74.3 to 100% vs. 59.0 to 88.9%; P<.05). However, the percentiles displayed more specificity to identify these alterations (46.2 to 62.2 vs. 21.3 to 46.9; P<.05). Area under the curve analysis showed that WHtR >0.5 can more readily detect hypertriglyceridemia (0.642), hypoalphalipoproteinemia (0.700), and a combination of two or more metabolic abnormalities (0.661), whereas WC >90th percentile, according to Klünder, better detected hyperglycemia (0.555). CONCLUSION WHtR >0.5 is a sensitive measure to identify pediatric patients with cardiometabolic alterations, despite its low specificity, and is a useful diagnostic tool to detect populations at risk. Based on the results of this study, we recommend preferential use of the Klünder waist circumference references over the Fernández method in Mexican pediatric populations. ABBREVIATIONS AUC = area under the curve BMI = body mass index HDL = high-density lipoprotein IDF = International Diabetes Federation LDL = low-density lipoprotein MS = metabolic syndrome NCHS = National Center for Health Statistics ROC = receiver operating characteristic WC = waist circumference WHO = World Health Organization WHtR = waist-to-height ratio.
Optimal thresholds for GMD decoding with ℓ+1 over ℓ-extended Bounded Distance decoders

We investigate threshold-based multi-trial decoding of concatenated codes with an inner Maximum-Likelihood decoder and an outer error/erasure ℓ+1 over ℓ-extended Bounded Distance decoder, i.e. a decoder which corrects ε errors and τ erasures if ℓ+1 over ℓε+τ ≤ d<sup>o</sup>−1, where d<sup>o</sup> is the minimum distance of the outer code and ℓ ∈ ℕ\{0}. This is a generalization of Forney's GMD decoding, which was considered only for ℓ = 1, i.e. outer Bounded Minimum Distance decoding. One important example for ℓ+1 over ℓ-extended Bounded Distance decoders is decoding of ℓ-Interleaved Reed-Solomon codes. Our main contribution is a threshold location formula, which allows to optimally erase unreliable inner decoding results, for a given number of decoding trials and parameter ℓ. Thereby, the term optimal means that the residual codeword error probability of the concatenated code is minimized. We give an estimation of this probability for any number of decoding trials.
The application of motion capture to embodied music cognition research

Thompson, Marc R. The application of motion capture to embodied music cognition research Jyväskylä: University of Jyväskylä, 2012, 86 p. (Jyväskylä Studies in Humanities ISSN 1459-4331; 176) ISBN 978-951-39-4689-0 (nid.) ISBN 978-951-39-4690-6 (PDF) Music and expressive body movements are inseparable. Musicians use movements to convey emotional expressivity, conductors use gestures to convey musical structure, and co-performers rely on corporeality to maintain group cohesion. Additionally, the spontaneously-produced movements that occur when listening to music appear to naturally synchronize with the musical pulse. Despite this tendency common among most people, movement patterns appear to be highly individualistic and perhaps related to expressive cues inherent in the music. A growing awareness of the significant role that expressive body movement plays in music-related activities has given rise to the application of embodied cognition to music. Embodied cognition is the view that knowledge is attained through sensorimotor representations of the world and that the human body acts as the main mediator between our thoughts and the environment. Music-related activities such as performance and dance are excellent examples embodied cognition, as they require online tracking of perceptual stimuli that is in turn being augmented by our own actions. Furthermore, the embodied approach to music assumes that we can interact with music at different levels of engagement ranging from synchronization with low-level features such as the beat to empathizing with the music’s higherlevel features such as expressive intentions. In both cases, musical meaning is developed through goal-directed corporeal actions, which both react and contribute to musical experiences. The study of such phenomena has greatly benefited from advances in optical motion capture systems, which can track movements with a high degree of precision. For analysing the movements, semantically significant features are then extracted from the raw motion capture data. These variables can describe the kinematics, kinetic or other behavioural features of musicians and dancers, and be subjected to an infinite variety of analysis methods. The aim of this thesis is to demonstrate, through experimental research, some applications of motion capture within the area of embodied music cognition. Across six independent studies, four music-related activities were analysed: piano performance, conducting gestures, choreographed choral performance and music-induced movements.
Intraoperative cardiac troponin T release and lactate metabolism during coronary artery surgery: comparison of beating heart with conventional coronary artery surgery with cardiopulmonary bypass

OBJECTIVE To compare cardiac troponin T release and lactate metabolism in coronary sinus and arterial blood during uncomplicated coronary grafting on the beating heart with conventional coronary grafting using cardiopulmonary bypass. DESIGN A prospective observational study with simultaneous sampling of coronary sinus and arterial blood: before and 1, 4, 10, and 20 minutes after reperfusion for analysis of cardiac troponin T and lactate. Cardiac troponin T was also analysed in venous samples taken 3, 6, 24, 48, and 72 hours after surgery. SETTING Cardiac surgical unit in a tertiary referral centre. PATIENTS 18 patients undergoing coronary grafting on the beating heart (10 single vessel and eight two-vessel grafting) and eight undergoing two-vessel grafting with cardiopulmonary bypass. RESULTS Cardiac troponin T was detected in coronary sinus blood in all patients by 20 minutes after beating heart coronary artery surgery before arterial concentrations were consistently increased. Peak arterial and coronary sinus cardiac troponin T values on the beating heart during single (0.03 (0 to 0.05) and 0.09 (0.07 to 0.16 μg/l, respectively) and two-vessel grafting (0.1 (0.07 to 0.11) and 0.19 (0.14 to 0.25) μg/l) were lower than the values obtained during cardiopulmonary bypass (0.64 (0.52 to 0.72) and 1.4 (0.9 to 2.0) μg/l) (p < 0.05). The area under the curve of venous cardiac troponin T over 72 hours for two-vessel grafting on the beating heart was less than with cardiopulmonary bypass (13 (10 to 16) v 68 (26 to 102) μg. h/l) (p < 0.001). Lactate extraction began within one minute of snare release during beating heart coronary surgery while lactate was still being produced 20 minutes after cross clamp release following cardiopulmonary bypass. CONCLUSIONS Lower intraoperative and serial venous cardiac troponin T concentrations suggest a lesser degree of myocyte injury during beating heart coronary artery surgery than during cardiopulmonary bypass. Oxidative metabolism also recovers more rapidly with beating heart coronary artery surgery than with conventional coronary grafting. Coronary sinus cardiac troponin T concentrations increased earlier and were greater than arterial concentrations during beating heart surgery, suggesting that this may be a more sensitive method of intraoperative assessment of myocardial injury.
SOME UNEXPECTED CONSEQUENCES OF IMPLEMENTING GENDER "NEUTRAL" REPRODUCTIVE PROGRAMS AND POLICIES

Historically, sexual and reproductive health programs in Mexico and the U.S. all but ignored male partners. The past decade’s significant shift to accord greater attention to men, however, may paradoxically subordinate women’s interests, goals, and needs. We illustrate this observation with data from a study of 156 women of Mexican background and their male partners in a California program offering prenatal genetic testing and abortion for birth anomalies in “high risk” pregnancies. When genetic counselors sensed ambivalence from women, they clearly allied themselves with the male partners to gain consent for procedures. The resultant male empowerment, coupled with problematical fetal diagnoses, could ignite or exacerbate domestic conflict.
Nonstationary Logistic Regression

In this paper, we consider the logistic regression model with an integrated regressor driven by a general linear process. In particular, we derive the limit distributions of the nonlinear least squares (NLS) estimators and their t-ratios of the parameters in the model. It is shown that the NLS estimators are generally not efficient. Moreover, the t-ratios for the level parameters have limit distributions that are nonnormal and dependent upon nuisance parameters, due to the asymptotic correlation between the innovations of the regressor and the regression errors. We propose an efficient NLS procedure to deal with the inefficiency of the estimators and inferential difficulty. The new NLS procedure yields estimators that are efficient and have asymptotically normal t-ratios. The finite sample properties of the usual and efficient NLS estimators and their t-statistics are investigated through Monte Carlo simulations.
The Adaptive Place Advisor: A Conversational Recommendation System

In this paper, we describe the Adaptive Place Advisor, a conversational recommendation system designed to help users decide on a destination. We view the selection of destinations as an interactive, conversational process, with the advisory system inquiring about desired item characteristics and the human responding. The user model, which contains preferences regarding items, attributes, values and value combinations, is also acquired during the conversation. The system enhances the user’s requirements with the user model and retrieves suitable items from a case-base. If the number of items found by the system is unsuitable (too high, too low) the next attribute to be constrained or relaxed is selected based on the information gain associated with the attributes. We also describe the current status of the system and future work.
New Fimbrial Gene Cluster of S-Fimbrial Adhesin Family

ABSTRACT Fimbrial adhesins that mediate attachment to host cells are produced by most virulent Escherichia coli isolates. These virulence factors play an important role in the initial stages of bacterial colonization and also in determination of the host and tissue specificity. Isolates belonging to serotype O78 are known to cause a large variety of clinical syndromes in farm animals and humans and have been shown to produce several types of adherence fimbriae. We studied the fimbrial adhesin from an avian septicemic E. coliisolate of serotype O78. Analysis of the genetic organization of thefac (fimbria of avian E. coli) gene cluster indicates that it belongs to the S-fimbrial adhesin family. Seven open reading frames coding for major and minor structural subunits were identified, and most of them showed a high degree of homology to the corresponding Sfa and Foc determinants. The least-conserved open reading frame was facS, encoding a protein known to play an important role in determining adherence specificity in other S-fimbrial gene clusters.
Cytoskeleton Reorganization as an Alternative Mechanism of Store-Operated Calcium Entry Control in Neuroendocrine-Differentiated Cells

Neuroendocrine differentiation (NED) is a hallmark of advanced androgen-independent prostate cancer, for which no successful therapy exists. NED tumour cells escape apoptotic cell death by alterations of Ca2+ homeostasis where the store-operated Ca2+ entry (SOCE) is known to be a key event. We have previously shown that the downregulation of Orai1 protein representing the major molecular component of endogenous SOCE in human prostate cancer cells, and constituting the principal source of Ca2+ influx used by the cell to trigger apoptosis, contributes to the establishment of an apoptosis-resistant phenotype (Cell Death Dis. 2010 Sep 16;1:e75.). Here, we report for the first time that the decrease of SOCE during NED may be caused by alternative NED-induced mechanism involving cytoskeleton reorganisation. NED induced by androgen deprivation resulted in a decrease of SOCE due to cortical F-actin over-polymerization which inhibits thapsigargin-induced SOCE. The disruption of F-actin polymerization by Cytochalasin D in NED cells restored SOCE, while the induction of F-actin polymerization by jasplakinolide or calyculin A diminished SOCE without changing the expression of key SOCE players: Orai1, STIM1, and TRPC1. Our data suggest that targeting cytoskeleton-induced pathways of malignant cells together with SOCE-involved channels may prove a useful strategy in the treatment of advanced prostate cancer.
Maximum-Likelihood Timing/Channel Estimation for OFDM Systems with Cyclic Training Symbols

We present a new algorithm for joint timing and channel estimation in OFDM systems with cyclic training symbols. The proposed algorithm employs multiple signal classification (MUSIC) approach for coarse timing estimation and then refines the timing/channel estimation by applying the generalized maximum likelihood rule (GMLR) within a symbol period around the coarse timing for different channel lengths. We reveal that the likelihood corresponding to different shift positions and channel lengths can be conveniently computed from a single N-length channel estimate, which considerably reduces the computational complexity and thus makes the refined search over long training symbols feasible.
Family pairwise search with embedded motif models

MOTIVATION Statistical models of protein families, such as position-specific scoring matrices, profiles and hidden Markov models, have been used effectively to find remote homologs when given a set of known protein family members. Unfortunately, training these models typically requires a relatively large set of training sequences. Recent work (Grundy, J. Comput. Biol., 5,<479-492, 1998) has shown that, when only a few family members are known, several theoretically justified statistical modeling techniques fail to provide homology detection performance on a par with Family Pairwise Search (FPS), an algorithm that combines scores from a pairwise sequence similarity algorithm such as BLAST. RESULTS The present paper provides a model-based algorithm that improves FPS by incorporating hybrid motif-based models of the form generated by Cobbler (Henikoff and Henikoff, Protein Sci., 6, 698-705, 1997). For the 73 protein families investigated here, this cobbled FPS algorithm provides better homology detection performance than either Cobbler or FPS alone. This improvement is maintained when BLAST is replaced with the full Smith-Waterman algorithm. AVAILABILITY http://fps.sdsc. edu
Remarkable moments: communicating trust in the relationship between the child with autism and the parent/caregiver

OF THE THESIS Remarkable Moments: Communicating Trust in the Relationship between the Child with Autism and the Parent/Caregiver by Sandra L. Weber Master of Arts in Interdisciplinary Studies San Diego State University, 2011 Very little solid scientific research has been conducted that directly documents a specific neurobiological structure in the human brain, regulating the innate perception of “basic trust. ” As an alternative, researchers are pursuing studies in analogous components of the “trust factor” to answer the question, “is there a biological basis for ‘basic trust’? ” Because perceived caregiver trust is a key component in autistic behavior remediation, this study affirms, articulates, and expands on the idea that there are actual biological indicators that reflect “basic trust. ” In addition to synthesizing previous applicable research regarding Autism Spectrum Disorder, this study illustrates the ways in which trust is communicated between parent/caregiver and the child with autism. To explore this topic, the study gathered both qualitative and quantitative information using a demographic survey and interview format. The participants of this phenomenological qualitative investigation consisted of twelve parent/caregivers whose children had been professionally diagnosed with autism. Collected quantitative demographic survey data and in-depth qualitative narrative information was evaluated for common themes within the respective parenting experiences. The long term benefit of illuminating the importance of trust formation in the success of therapeutic autism intervention programs outweighed the potential risk of emotional discomfort from retelling/reliving of some unpleasant memories. Anonymity was preserved through coding of the informational materials for the parent/caregiver participants. Interviews were done at a location and time selected by each volunteer to maximize personal comfort, convenience, and to promote the narrative process. None of the current commercially-based methods for therapeutic intervention have produced consistent results in every diagnosed child. Regardless of the degree of disability, the ultimate goal for the ASD child is behavioral compliance. Without it, appropriate socialization at any level is impossible to achieve. The underpinning for behavioral compliance that leads to socialization is the ability to experience a sense of “basic trust” and to perceive the caregiver(s) as trustworthy.
Comparative study of four rice cultivars with different levels of cadmium tolerance

Cadmium (Cd) has been identified as a significant pollutant due to its high solubility in water and soil and high toxicity to plants and animals. Rice, as one of the most important food crops, is grown in soils with variable levels of Cd and therefore, is important to discriminate the Cd tolerance of different rice cultivars to determine their suitability for cultivation in Cd-contaminated soils. This study investigates the primary mechanisms employed by four rice cultivars in attaining Cd tolerance. HA63 cultivar reduces Cd uptake by increasing Fe absorption through activation of phytosiderophores. T3028 cultivar accumulates the highest level of Cd in leaves while also activating its reactive oxygen species (ROS) scavenging system, including antioxidant enzymes and phytochelatins. In some rice cultivars (such as HA63), a cyanide-resistant respiration mechanism, important in Cd detoxification, was also promoted under the Cd stress. In conclusion, different rice cultivars may adopt different biochemical strategies and respond with different efficiency to Cd stress.
Frames of reference in language, culture, and cognition:

• the big questions – what is the role of culture in cognition? – does speaking particular languages influence the way the speakers think? • the subsidiary questions – are practices of language use contact-diffused? – can such practices constitute areal features? • a domain in which to look for answers: spatial frames of reference 3 Spatial reference frames in language, culture, and cognition (cont.)