Miracle-dz/UniFAR-FTUs huggingface dataset:
Cloning and characterization of styrene catabolism genes from Pseudomonas fluorescens ST

A gene bank from Pseudomonas fluorescens ST was constructed in the broad-host-range cosmid pLAFR3 and mobilized into Pseudomonas putida PaW340. Identification of recombinant cosmids containing the styrene catabolism genes was performed by screening transconjugants for growth on styrene and epoxystyrene. Transposon mutagenesis and subcloning of one of the selected genome fragments have led to the identification of three enzymatic activities: a monooxygenase activity encoded by a 3-kb PstI-EcoRI fragment and an epoxystyrene isomerase activity and an epoxystyrene reductase activity encoded by a 2.3-kb BamHI fragment. Escherichia coli clones containing the 3-kb PstI-EcoRI fragment were able to transform styrene into epoxystyrene, and those containing the 2.3-kb BamHI fragment converted epoxystyrene into phenylacetaldehyde or, only in the presence of glucose, into 2-phenylethanol. The three genes appear to be clustered and are probably encoded by the same DNA strand. In E. coli, expression of the epoxystyrene reductase gene was under the control of its own promoter, whereas the expression of the other two genes was dependent on the presence of an external vector promoter.
Different modes of thought during the creative process

Creativity is most often defined as the ability to produce ideas that are both novel and useful. Consistent with this twofold definition, psychological theories have suggested that creativity involves a twofold process characterized by a generative (or associative) component that facilitates the production of novel ideas, and an evaluative (or analytic) component that enables the assessment of these ideas as to their usefulness. To investigate this, the present study employed a novel paradigm that was specifically designed to allow for separately examining the generative and evaluative components of the creative process. Functional magnetic resonance imaging (fMRI) was used to identify the contribution of particular brain regions to creative generation and evaluation. Participants were presented with short book descriptions and, using an fMRI-compatible drawing tablet, designed corresponding book cover illustrations while alternating between the generation and evaluation of ideas. Creative generation and evaluation were associated with recruitment of distinct neural circuits, with generation preferentially recruiting medial temporal lobe regions, and evaluation showing joint recruitment of executive and default network regions. These findings suggest that the medial temporal lobe may play an important role in the generation of novel ideas, and that creative evaluation may extend beyond deliberate and cognitive analytical processes supported by executive resources to include spontaneous, affective, and visceroceptive analytical processes. In summary, separating and alternating between generative and evaluative modes during a creative task helped to provide a better characterization of the contributions of creativity-related brain areas to the creative process, which had previously only been inferred indirectly. The results of this study suggest that creative thinking recruits a unique configuration of neural processes not typically used together in more traditional tasks.
A Metastasis or a Second Independent Cancer ? Evaluating the Clonal Origin of Tumors Using Array-CGH Data

When a cancer patient develops a new tumor it is necessary to determine if this is a recurrence (metastasis) of the original cancer, or an entirely new occurrence of the disease. This is accomplished by assessing the histo-pathology of the lesions, and it is frequently relatively straightforward. However, there are many clinical scenarios in which this pathological diagnosis is difficult. Since each tumor is characterized by a genetic fingerprint of somatic mutations, a more definitive diagnosis is possible in principle in these difficult clinical scenarios by comparing the fingerprints. In this article we develop and evaluate a statistical strategy for this comparison when the data are derived from array comparative genomic hybridization, a technique designed to identify all of the somatic allelic gains and losses across the genome. Our method involves several stages. First a segmentation algorithm is used to estimate the regions of allelic gain and loss. Then the broad correlation in these patterns between the two tumors is assessed, leading to an initial likelihood ratio for the two diagnoses. This is then further refined by comparing in detail each plausibly clonal mutation within individual chromosome arms, and the results are aggregated to determine a final likelihood ratio. The method is employed to diagnose patients from several clinical scenarios, and the results show that in many cases a strong clonal signal emerges, occasionally contradicting the clinical diagnosis. The “quality” of the arrays can be summarized by a parameter that characterizes the clarity with which allelic changes are detected. Sensitivity analyses show that most of the diagnoses are robust when the data are of high quality. clonality-cgh-jasa 07/31/08 A Metastasis or a Second Independent Cancer? Evaluating the Clonal Origin of Tumors Using ArrayCGH Data Irina Ostrovnaya, Adam B. Olshen, Venkatraman E. Seshan, Irene Orlow, Donna G. Albertson, Colin B. Begg 1. Memorial Sloan-Kettering Cancer Center, New York 2. Columbia University, New York 3. University of California, San Francisco Correspondence to: Colin B. Begg, Department of Epidemiology and Biostatistics, 307 East 63rd Street, New York, NY 10021, beggc@mskcc.org Hosted by The Berkeley Electronic Press
[Diffusion MRI and cerebral ischemia. When to calculate the coefficient of diffusion?].

INTRODUCTION There are two types of diffusion images: so-called "diffusion-weighted" images (DWI) and apparent diffusion coefficient (ADC) images. For certain authors, ADC mapping is crucial for interpreting diffusion images while for others the ADC map adds no further sensitivity or specificity compared with diffusion weighted images. The objective of this work was to determine those situations where ADC mapping modifies image interpretation. MATERIAL AND METHODS T2-weighted and diffusion-weighted (DIF) MRI sequences were acquired in 197 patients with suspected cerebral ischemia (< or = 48 hr). For each lesion (239 lesions in the 197 patients), we analyzed MRI interpretation with and without ADC mapping and compared the interpretations with the final diagnosis established on clinical data and complementary explorations. RESULTS We observed 3 groups. In group A (36% of the lesions), ADC mapping did not change image interpretation. This group was subdivided into 3 subgroups. A1: T2 and DIF weighted images are normal: no lesions and normal ACD map (n = 38 patients); A2: High intensity signal on T2 and low intensity signal on DIF: ischemic sequelae, ADC always increased (n = 32 lesions); A3: T2 normal and high intensity signal on DIF: hyper acute ischemia and ADC always decreased (n = 16 patients) In group B (high intensity signal on T2 and DIF, 54.5% of the lesions), ADC mapping changed the MRI interpretation: there was acute ischemia if the ADC was decreased (n = 113) and "pseudo-ischemic" lesions if the ADC was normal or increased (n = 17 patients). Group C was comprised of 23 lesions with a false negative ADC (9.5%). These lesions were always small recent ischemic lesions (< or = 5 mm) with a high intensity signal on DIF and a strictly normal ADC map. CONCLUSION ADC mapping was found to be useful in 54.5% of the lesions and should not be considered as solely a research tool but also as a useful tool for routine clinical practice.
SPA: Short peptide analyzer of intrinsic disorder status of short peptides

Disorder prediction for short peptides is important and difficult. All modern predictors have to be optimized on a preselected dataset prior to prediction. In the succeeding prediction process, the predictor works on a query sequence or its short segment. For implementing the prediction smoothly and obtaining sound prediction results, a specific length of the sequence or segment is usually required. The need of the preselected dataset in the optimization process and the length limitation in the prediction process restrict predictors’ performance. To minimize the influence of these limitations, we developed a method for the prediction of intrinsic disorder in short peptides based on large dataset sampling and statistics. As evident from the data analysis, this method provides more reliable prediction of the intrinsic disorder status of short peptides.
Vascular Endothelial Growth Factor in Dialysate in Relation to Intensity of Peritoneal Inflammation

Background Peritoneal inflammation may induce changes in peritoneal microvessels, including neoangiogenesis/vasculogenesis, leading to increased peritoneal solute transport rate (PSTR) and loss of ultrafiltration capacity. We hypothesized that an inflammatory reaction in the peritoneal cavity during peritonitis induces increased synthesis of vascular endothelial growth factor (VEGF). We therefore studied the relationship between peritoneal inflammation markers, VEGF, and transport of fluid and solutes in rats during acute peritoneal inflammation induced by lipopolysaccharide (LPS) added to standard glucose-based dialysis solution. Methods Under ether anesthesia, male Wistar rats were injected intraperitoneally with 30 mL Dianeal 3.86% without (Control; n=6) or with LPS (μg/mL): 0.001 (LPS 0.001; n=6), 0.01 (LPS 0.01; n=7), 0.1 (LPS 0.1; n=7), 1.0 (LPS 1.0; n=8). After 8 hours, dialysate volume (IPV), peritoneal solute transport rate (PSTR) and dialysate cell count (DCC) were measured and effluent samples were collected. Results LPS i.p. resulted in increased PSTR and decreased IPV (p<0.005). DCC (cells/μL) and the neutrophil/macrophage ratio were higher for all LPS concentrations compared to the control group. After 8 hours, LPS-exposed rats had significantly higher dialysate levels of all investigated cytokines (TNF-α, MCP-1 and IL-10) than the control group. Addition of LPS resulted in increased dialysate VEGF concentrations (pg/mL) (LPS 0.001, 28.2±5.9; LPS 0.01, 38.9±11.6; LPS 0.1, 43.0±5.9; LPS 1.0, 46.6±11.3; Control, 14.5±9.8; p<0.0005 for all LPS vs. Control). Conclusions The infusion of Dianeal 3.86% with different doses of LPS induced a strong acute intraperitoneal inflammatory reaction with increased DCC and cytokine levels, resulting in increased peritoneal solute transport and decreased IPV LPS induced a dose-dependent parallel increase of the intraperitoneal concentrations of MCP-1, IL-10 and TNF-α, as well as of VEGF. These results suggest that intraperitoneal VEGF synthesis is induced in response to inflammation, and that this may be an important component in the process leading to peritoneal transport alterations.
CS 224 W : Social and Information Network Analysis Reaction Paper

In this reaction paper, we investigate the property of self-similarity exhibited by various real-life networks, and the models that have been proposed to describe such networks. We begin with the paper [1], in which the authors analyzed metabolic networks in organisms. We next look at the self-similar structure seen in email networks and their comparison to river networks in [2]. In [3] this property of complex networks is studied further and a mechanism for the growth of such networks is proposed in [4]. Finally we look at more recent work in [5], [6] and [7] related to Kronecker Graphs, which have been shown to accurately model many properties of real-life networks with very few parameters. This reaction paper thus relates to the following concepts of networks studied in class: (a) Network connectivity (b) network diameter (c) network topology (d) clustering coefficient (e) decentralized search and (f) robustness.
Object-Centric Thermal Mapping: A wireless sensor network perspective

This work mainly focuses on developing a concept towards building an Object-Centric Thermal Mapping (OCT Map) environment based on the use of wireless sensor networks. The sensor network is represented through infrastructural sensors of any functional space like the cool-room or a food-store. These sensors facilitate initial values for the calculation of the temperature at a given location within the space. In this work, Artificial Neural Networks (ANN) are used for predicting the thermal map of a given space. It is found that the estimated temperature distributions at any arbitrary points have considerably low Root Mean Square Error (RMSE). However the accuracy of the prediction and number of infrastructural nodes are concerned, at 8 infrastructural nodes and the room volume of 4500m3, the temperature can be predicted with at least RMS error of 0.02°C. The results divulged that the design of using neural networks for temperature mapping is feasible.
The Round-Trip p-Center and Covering Problem on a Tree

A task performed by a vehicle consists of picking up goods at a given client and delivering it to another client. The round-trip distance is the distance traveled by the vehicle between the departure from and the return to its depot. The round-trip p-center problem is to locate p depots with respect to a finite number of pairs of clients so as to minimize the maximum round-trip cost, which is defined as a nonlinear increasing function of the round-trip distance from the nearest depot. The round-trip covering problem is to find the minimum number of depots such that each round-trip cost is no more than a given constant. For both problems a dual problem is defined and in case the underlying network is a tree a strong duality result is proved. We give algorithms to solve both tree round-trip location problems in polynomial time.
Inter-Channel Nonlinear Interference Noise in WDM Systems: Modeling and Mitigation

We review the modeling of inter-channel nonlinear interference noise (NLIN) in fiber-optic communication systems, focusing on the accurate extraction of the NLIN variance, the dependence on modulation format, the role of nonlinear phase-noise, and the existence of temporal correlations. We show ways in which temporal correlations can be exploited for reducing the impact of NLIN, and discuss the prospects of this procedure in future systems.
Discrimination of Audio Signals Using Time-Frequency Distributions

Humans can discriminate speech from music easily in their mind without any influence of the mixed music. Due to the new techniques of analysis and synthesis of speech signals, the musical signal processing has gained particular weight, and therefore, the classical sound analysis techniques are used in processing music signals. Music art has a long and distinguished history. It goes back to the time of Greek and is developed through centuries in both the musical instruments and melodies. The problem of audio signal classification serves as the fundamental step towards the rapid growth in audio data volume [1], [2], and [3]. There are many kinds of music such as: Classical, Rock, Pop, Disco, Jazz, Country, Latin, Electronic, Arabic, etc. [4], [5], [6], [7], and [8]. Audio signals change continuously and non-deterministically with time [12]. Consequently they are usually characterized as time averages, and their relative amplitude and frequency contents can be easily specified. As an example, speech and music typically have strong low-frequency energy and progressively weaker high-frequency content [9], [10], [11], and [12]. The maximum frequency, fmax, of an audio signal varies according to audio signal kind; fmax equals 22 KHz in CD quality recording, 11 KHz in FM stereo broadcasting, 6 KHz in stereo or multi-loudspeaker recording, 5 KHz in mono-loudspeaker recording, and 4 kHz in the traditional telephone transmitting quality. A generalized frequency spectrum for audio signal is shown in Figure 1, and audio signals can be classified into the following classes: 1Speech signal compounded of single talker in specific time period. 2Completely music signal without any speech component. 3Mixture of single talker speech and background music. 4Songs; mixture of music with a singer voice. 5Singing without music. 6Abnormal music; uses acclaim cadence, single word cadence, human whistle sound, opposite reverberation or any non-music sound that been inserted as a basic tone of the music melody. These cadences cannot be generated by any of the ordinary musical instrument except modern Organ and mainly processed by a major help of computers. 7Speech signal compounded of two or more speakers talking simultaneously in a specific time period. A good algorithm for separating the sounds of two talkers taking simultaneously is using the cepstrum analysis. 8Non-speech and non-music signals: like car, motor, fan sounds, etc. 9Complex sound mixture like multi-speakers or multisingers with multi-music sources.
Thirty years of information literacy (1977—2007)

Over the last three decades, promotion of information literacy has become one of the main goals of librarians and academics. As the emergence of information technologies has raised new challenges and roles for users, information literacy has shifted from the concept of simple training to the provision of the skills and competencies that are critical to the improved use of information. A terminological, conceptual and statistical analysis of the main subjects related to information literacy, as well as its evolution over the last 30 years, is provided with the aim of illustrating how information literacy has been progressively incorporated into the library and academic fields.
Performance Enhancement in Double-Gated Poly-Si Nanowire Transistors With Reduced Nanowire Channel Thickness

A new method is proposed and successfully demonstrated for the fabrication of polycrystalline silicon (poly-Si) nanowire (NW) transistors with rectangular-shaped NW channels and two independent gates. The two independently controllable gates allow higher flexibility in device operation and provide a unique insight into the conduction mechanism of the NW device. Our results indicate that dramatic performance enhancement is feasible when the thickness of the NW channel is sufficiently thin, and the two conduction channels in the NW structure are operating simultaneously.
Effect of duration of upper- and lower-extremity rehabilitation sessions and walking speed on recovery of interlimb coordination in hemiplegic gait.

BACKGROUND AND PURPOSE The effects of different durations of rehabilitation sessions for the upper extremities (UEs) and lower extremities (LEs) on the recovery of interlimb coordination in hemiplegic gait in patients who have had a stroke were investigated. SUBJECTS AND METHODS Fifty-three subjects who had strokes involving their middle cerebral arteries were assigned to rehabilitation programs with (1) an emphasis on the LEs, (2) an emphasis on the paretic UE, or (3) a condition in which the paretic arm (UE) and leg (LE) were immobilized with an inflatable pressure splint (control treatment). The 3 treatment regimens were applied for 30 minutes, 5 days a week, during the first 20 weeks after onset of stroke. All subjects also participated in a rehabilitation program 5 days a week that consisted of 15 minutes of UE exercises and 15 minutes of LE exercises in addition to a weekly 11/2-hour session of training in activities of daily living. A repeated-measures design was used. Differences among the 3 treatment regimens were evaluated in terms of comfortable and maximal walking speeds. In addition, mean continuous relative phase (CRP) between paretic arm and leg (PAL) movements and nonparetic arm and leg (NAL) movements and standard deviations of CRP of both limb pairs as a measurement of stability (variability) were evaluated. RESULTS Comfortable walking speed improved in the group that received interventions involving the LEs compared with the group that received interventions involving the UEs and the group that received the control treatment. No differences among the 3 treatment conditions were found for the mean CRP of NAL and PAL as well as the standard deviation of CRP of both limb pairs. DISCUSSION AND CONCLUSION With the exception of an improved comfortable walking speed as a result of a longer duration of rehabilitation sessions, no differential effects of duration of rehabilitation sessions for the LEs and UEs on the variable we measured related to hemiplegic gait were found. Increasing walking speed, however, resulted in a larger mean CRP for both limb pairs, with increased stability and asymmetry of walking, indicating that walking speed influences interlimb coordination in hemiplegic gait.
Measuring effectiveness for best evidence medical education: a discussion

This paper considers how educational interventions should be evaluated for their effectiveness. Five levels of effectiveness are clarified and illustrated: outcomes, behaviour, learning, reaction and participation. These levels are then discussed, within the context of research evidence for education within the medical profession. Methodological and practical research conclusions are then drawn. From an analysis of over 300 abstracts the evidence shows that only limited research on healthcare outcomes has been undertaken, and there is considerable ambiguity over what constitutes an effectiveness measure. The benefits of a consistent set of terms are then considered. Finally, five key messages are distilled from the discussion and summarized.
On designing interactive systems that support creative problem solving in expert domains

Finding creative solutions to ill-structured problems is integral to the work in many expert domains. A common flaw of software tools that support this kind of work is to support mainly the detailed specification of a selected solution. To extend this support to the other processes of ill-structured problem-solving, I propose ten design principles, synthesized from results in diverse fields of research. These processes emphasize generating and comparing many potential solutions. To evaluate the principles’ effectiveness, I built two prototypes; quantitative and qualitative results from evaluations demonstrate benefits, including faster task completion and the consideration of a wider variety of solutions. As there is disagreement within human-computer interaction on how to conduct such broad-scoped research, I introduce a generic framework modelled on the legal system and Thagard’s explanatory coherence theory to structure this evidence into a compelling argument for the principles’ wider adoption.
The complete mitochondrial genome of a deep-water Baikalian amphipoda Brachyuropus grewingkii (Dybowsky, 1874)

Abstract In this study, we present a complete mitochondrial genome of a deep-water amphipoda Brachyuropus grewingkii (Dybowsky, 1874) from Lake Baikal. A circular mitochondrial DNA has 17,118 bp in length and contains 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, a putative control region, and five intergenic spacers. An extended control region and altered positions of some tRNA genes distinguish mitochondrial genome of B. grewingkii from the mitochondrial genomes described for other Baikalian amphipoda species.
Comparison of Three Depression Rating Scales

We directly compared scores on the self-rated Beck Depression Inventory with two other common rating scales that assess a wider range of psychopathology, including depression, the self-rated Symptom Check List-90—R (SCL-90—R), and the clinician-rated Brief Psychiatric Rating Scale for 71 inpatients who suffered from depression (n = 50) and other disorders. All measures of depression showed robust correlations among themselves. The self-rated scales correlated better between themselves than with the clinician-rated scale. Since the SCL-90—R assesses depression as well as the Beck inventories, is also a self-report instrument, yet provides a richer description of psychopathology with little extra effort, it may have some advantage over the latter.