Miracle-dz/UniFAR-FTUs huggingface dataset:
Nutritional Status and Amino Acids in Granulocytes and Plasma in Patients with Chronic Renal Disease and Varying Residual Renal Function

Background: Protein metabolism changes with loss of renal function resulting in deterioration of nutritional status. Whether changes in macroscopic (anthropometry and subjective global nutritional assessment (SGNA)) and cellular (plasma and granulocyte free amino acid concentration) nutritional status with loss of residual renal function are related is not known. Methods: Anthropometric variables, SGNA, and blood samples were measured after a night’s fast in 43 patients (age 57 years, median (range 27–77), 32 males and 11 females) with chronic renal disease. A 24-hour urine sample was collected the day before the study for calculation of creatinine clearance and protein nitrogen appearance rate. The patients were stratified according to creatinine clearance (group I: >35 ml/min/1.73 m2, group II 35–15 ml/min/1.73 m2, group III <15 ml/min/1.73 m2). Results: In males a significant lower body weight (p < 0.05) and upper mid-arm muscle area (p < 0.05) was found in group III compared to group I. SGNA indicated suboptimal nutritional status in 12 patients. In group I all had normal SGNA while in group II and group III, 26 and 57% respectively were malnourished. SGNA was significantly and negatively correlated to upper mid-arm muscle area (ρ = –0.37, p < 0.05) and percent body fat mass (ρ = –0.46, p < 0.01) and positively correlated to percent ideal body weight (ρ = 0.48, p < 0.01). Nine patients with malnutrition (M) were compared with 9 well-nourished (N) patients. They were comparable with respect to creatinine clearance (M: 13 ± 5 ml/min/1.73 m2; N: 16 ± 7 ml/min/1.73 m2), age and sex. In malnourished patients plasma concentration of nonessential amino acids was higher (23%, p < 0.05). The intracellular concentration was generally not affected except for sulfur amino acid methionine which was increased by a factor of 2.5 (p < 0.05) and taurine decreased by a factor of 1.6 (p < 0.05). Conclusion: Loss of renal residual function worsened both macroscopic and cellular nutritional status. SGNA correlated to objective measures of nutritional status and is clinically usable. In malnourished chronic renal patients, increased plasma concentration of nonessential amino acids was found which might indicate increased protein degradation.
Temperature and time efficient parallel test scheduling for 3D stacked SoCs

Today's VLSI circuits have improved immensely and have become very compact and complex. The advancements made are very fast and many designs and technologies have come up, System-in-a-package SiP, 3D-SoC, TSV based SoC to name a few. The complexity of circuits is increasing and with emphasis on less time to market, the number of defects and errors are increasing. This mandates a proper testing process to be adopted for all products. Testing is required to be performed on each manufactured product. At the same time it requires a low cost, highly efficient method to be adopted. It should involve good fault coverage, low cost and less time consuming. System on Chip is a design paradigm which involves integration of entire system onto a single chip. It can be a RAM, DRAM, CPU, UDL, analog, digital, A/D or D/A converters needed for any particular requirement. In this paper we have worked on test scheduling of 3D SoCs with thermal and time constraints. The circuits used have been built using benchmark SoC circuits taken from ITC'02 benchmark circuits. Various circuits have been stacked on top of each other for making 3D circuits. The method of test scheduling proposed has been compared with the sequential method of testing which involves testing of all cores of a SoC completely and then taking other circuit. The method proposed in this work gives good results and does not result in hotspot formation.
Genome-Wide Identification and Characterization of BrrTCP Transcription Factors in Brassica rapa ssp. rapa

The teosinte branched1/cycloidea/proliferating cell factor (TCP) gene family is a plant-specific transcription factor that participates in the control of plant development by regulating cell proliferation. However, no report is currently available about this gene family in turnips (Brassica rapa ssp. rapa). In this study, a genome-wide analysis of TCP genes was performed in turnips. Thirty-nine TCP genes in turnip genome were identified and distributed on 10 chromosomes. Phylogenetic analysis clearly showed that the family was classified as two clades: class I and class II. Gene structure and conserved motif analysis showed that the same clade genes have similar gene structures and conserved motifs. The expression profiles of 39 TCP genes were determined through quantitative real-time PCR. Most CIN-type BrrTCP genes were highly expressed in leaf. The members of CYC/TB1 subclade are highly expressed in flower bud and weakly expressed in root. By contrast, class I clade showed more widespread but less tissue-specific expression patterns. Yeast two-hybrid data show that BrrTCP proteins preferentially formed heterodimers. The function of BrrTCP2 was confirmed through ectopic expression of BrrTCP2 in wild-type and loss-of-function ortholog mutant of Arabidopsis. Overexpression of BrrTCP2 in wild-type Arabidopsis resulted in the diminished leaf size. Overexpression of BrrTCP2 in triple mutants of tcp2/4/10 restored the leaf phenotype of tcp2/4/10 to the phenotype of wild type. The comprehensive analysis of turnip TCP gene family provided the foundation to further study the roles of TCP genes in turnips.
Functional implications of the influence of ABCA1 on lipid microenvironment at the plasma membrane: a biophysical study

The ABCA1 transporter orchestrates cellular lipid homeostasis by promoting the release of cholesterol to plasmatic acceptors. The molecular mechanism is, however, unknown. We report here on the biophysical analysis in living HeLa cells of the ABCA1 lipid microenvironment at the plasma membrane. The modifications of membrane attributes induced by ABCA1 were assessed at both the outer and inner leaflet by monitoring either the lifetime of membrane inserted fluorescent lipid analogues by fluorescence lifetime imaging microscopy (FLIM) or, respectively, the membrane translocation of cationic sensors. Analysis of the partitioning of dedicated probes in plasma membrane blebs vesiculated from these cells allowed visualization of ABCA1 partitioning into the liquid disordered‐like phase and corroborated the idea that ABCA1 destabilizes the lipid arrangement at the membrane. Specificity was demonstrated by comparison with cells expressing an inactive transporter. The physiological relevance of these modifications was finally demonstrated by the reduced membrane mobility and function of transferrin receptors under the influence of an active ABCA1. Collectively, these data assess that the control of both transversal and lateral lipid distribution at the membrane is the primary function of ABCA1 and positions the effluxes of cholesterol from cell membranes downstream to the redistribution of the sterol into readily extractable membrane pools. —Zarubica, A. , Plazzo, A.P., Stockl, M. , Trombik, T. , Hamon, Y. , Muller, P., Pomorski, T. , Herrmann, A. , Chimini, G. Functional implications of the influence of ABCA1 on lipid microenvironment at the plasma membrane: a biophysical study. FASEB J. 23, 1775–1785 (2009)
Rapid cell population identification in flow cytometry data

We have developed flowMeans, a time‐efficient and accurate method for automated identification of cell populations in flow cytometry (FCM) data based on K‐means clustering. Unlike traditional K‐means, flowMeans can identify concave cell populations by modelling a single population with multiple clusters. flowMeans uses a change point detection algorithm to determine the number of sub‐populations, enabling the method to be used in high throughput FCM data analysis pipelines. Our approach compares favorably to manual analysis by human experts and current state‐of‐the‐art automated gating algorithms. flowMeans is freely available as an open source R package through Bioconductor. © 2010 International Society for Advancement of Cytometry
HIV-1 Drug-Resistance Mutations among Newly Diagnosed Patients before Scaling-Up Programmes in Burkina Faso and Cameroon

We analysed whether mutations associated with resistance to antiretroviral (ARV) drugs circulate among treatment-naive HIV-1-infected individuals at a period when these drugs started to become more widely available in Africa. Overall, major resistance mutations in the pol gene, as defined by the International AIDS Society Resistance Testing-USA panel, were observed in 16 treatment-naive individuals. Eight of the 97 patients tested in Burkina Faso bore mutations conferring resistance to one drug class of ARV drugs: two to nucleoside reverse transcriptase inhibitors (NRTIs; M41L [n=1], M41L+T69S [n=1]), four to non-NRTIs (NNRTIs; V106A/V [n=1] and V108I [n=3]) and two to protease inhibitors (PIs; L33F [n=2]). In Cameroon, resistance mutations were identified in 8 of 102 patients: three to PIs (M46I/L [n=2], L33F [n=1]), three to NRTIs (T69N/T [n=1], M184V [n=1], A62V [n=1]) and two to NNRTIs (P236L [n=1], V108I [n=1]). It is important to note that not all geno-typic drug-resistance algorithms give similar interpretations to the observed mutations. Population surveillance for ARV drug resistance is required and should be included in all implementation programmes.
Solvent effect on cDNA-expressed human sulfotransferase (SULT) activities in vitro.

Sulfation is an important reaction in the biotransformation of steroid hormones, neurotransmitters, drugs, and other xenobiotics, yet little is known about the effects of organic solvents on sulfotransferase (SULT) activities in vitro. Initial experiments found that surprisingly low levels of solvent had dramatic effects on sulfotransferase activity. Consequently, we evaluated the effects of five commonly used solvents (methanol, ethanol, acetonitrile, dimethyl sulfoxide, and dimethyl formamide) on activities of cDNA-expressed sulfotransferase isozymes 1A1 (4-nitrophenol sulfation), 1A3 (dopamine sulfation), 1E1 (ethynylestradiol sulfation), and 2A1 (dehydroepiandrosterone sulfation). In addition, 1-hydroxypyrene was used as a general fluorescent probe for all four sulfotransferase isoforms examined. When substrates were present at their respective isoform-specific Km values, methanol and ethanol (0.4%, v/v) generally had less effect than acetonitrile, dimethyl sulfoxide, and dimethyl formamide on sulfotransferase activities. Acetonitrile, a commonly used solvent in cytochrome P450 studies, inhibited SULT1A1 activities (approximately 40%) at 0.4% (v/v), but activated SULT1E1-mediated 1-hydroxypyrene sulfation approximately 2.6-fold. Assuming a two-site kinetic model, studies revealed that solvent affected Vmax1, Vmax2, and the Ki value of 1-hydroxypyrene sulfation mediated by SULT1E1. In contrast, the Km value was not affected, suggesting that solvent may potentially alter binding interactions of the second substrate molecule, but not the first. Additional experiments with expressed SULT1A1, supplemented with control protein, revealed that the inhibitory effect of solvent (0.4%, v/v) was reduced to <15% for all solvents examined. Thus, it is recommended that ethanol is used as the preferred solvent vehicle and that incubations with expressed enzyme contain >12 microg/ml total protein.
Distributed Development and Product Line Decisions

Distributed product development is becoming increasingly prevalent in a number of industries. We study how the global distribution of product development impacts the profit‐maximizing product line that a firm offers. Specifically, we formulate a model to understand the linkage between cost arbitrage as a driver of distributed development and consequent market implications such as customer perceived quality loss to remotely developed products. Analysis of the model reveals that a firm should expand the product line for a development‐intensive good only at intermediate values of cost advantage and quality loss. We modify the base model to include development capacity constraints as a driver of distributed development and find that the results are robust to this change. Our analysis affirms the need for product managers to incorporate the implications of distributed development in making their product line design decision.
Laparoscopic adrenalectomy for adrenal tumors in children: a case series.

PURPOSE The aims of this study were to present our experience with children who underwent laparoscopic adrenalectomy for adrenal tumors over a 4-year period, discuss the technical aspects of the procedure, and review the current literature. METHODS We performed a retrospective review of all laparoscopic adrenalectomies performed at our institution between August 2003 and August 2007. RESULTS Eight patients underwent laparoscopic adrenalectomy. There were 6 girls and 2 boys. The median age was 14.5 years (range, 2-18). The median weight was 53.5 kg (range, 13-73). We performed 6 left and 2 right adrenalectomies. A lateral transperitoneal approach was used in all cases. All left adrenalectomies required three ports, while the right adrenalectomies were completed with four ports. All cases were done with two or three 5-mm ports and one 10-mm port. Tumor size ranged from 3 to 7 cm maximum diameter. The mean operative time was 99 minutes (range, 58-140). There were no complications. Blood loss was minimal in all cases and none required a conversion to open. All patients resumed oral feeds immediately after surgery. The mean hospital stay was 1.5 days (range, 1-2). The need for narcotic analgesia was minimal. Final diagnoses included: adrenal cortical adenoma (n = 4), ganglioneuroma (n = 2), pheochromocytoma (n = 1), and neuroblastoma (n = 1). CONCLUSIONS Laparoscopic adrenalectomy appears to be a safe, effective technique in children with small, well-circumscribed adrenal masses. The lateral transperitoneal approach offers optimal visualization and excellent outcomes in terms of minimal discomfort, rapid recovery, and excellent cosmesis.
Distributed Beamforming and Autonomous Participation Decision Making in Cooperative CR Systems in Presence of Asynchronous Interference

We propose a distributed beamforming for cooperative cognitive radio (CR) networks, that reduces the required feedback overhead in terms of sharing the channel state information (CSI) between the cooperating CR relays. Assuming the reciprocity of the channels of each cooperating CR node toward the CR receiver, as well as toward the primary receiver, the proposed beamforming technique only requires sharing the location information of the CR relays among the cooperating CR relays, rather than the global CSI. Reducing the required feedback overhead provides enhanced scalability of the cooperative CR network with lower deployment cost. In this paper, we also propose two autonomous decision making strategies that can help each CR user to independently decide whether to participate in the cooperative transmission or not. This participation decision is tackled from a game theoretic approach, by quantifying the reward and cost functions of each CR relay. The first proposed strategy, named regret testing-based strategy, is proved to asymptotically achieve an approximate Nash equilibrium state of the system. However, it has higher complexity and slower convergence time. So we also propose a suboptimal decision making strategy, named learning-based strategy, that has lower complexity and faster convergence time.
High-performance gene name normalization with GENO

MOTIVATION The recognition and normalization of textual mentions of gene and protein names is both particularly important and challenging. Its importance lies in the fact that they constitute the crucial conceptual entities in biomedicine. Their recognition and normalization remains a challenging task because of widespread gene name ambiguities within species, across species, with common English words and with medical sublanguage terms. RESULTS We present GeNo, a highly competitive system for gene name normalization, which obtains an F-measure performance of 86.4% (precision: 87.8%, recall: 85.0%) on the BioCreAtIvE-II test set, thus being on a par with the best system on that task. Our system tackles the complex gene normalization problem by employing a carefully crafted suite of symbolic and statistical methods, and by fully relying on publicly available software and data resources, including extensive background knowledge based on semantic profiling. A major goal of our work is to present GeNo's architecture in a lucid and perspicuous way to pave the way to full reproducibility of our results. AVAILABILITY GeNo, including its underlying resources, will be available from www.julielab. de. It is also currently deployed in the Semedico search engine at www.semedico. org.
Cannabis, Cocaine and Jobs

This paper uses a dataset collected among inhabitants of Amsterdam, to study the employment effects of the use of cannabis and cocaine. For females no negative effects of drug use on the employment rate are found. For males there is a negative relationship between past cannabis and cocaine use and employment. However, this relationship has to do with correlation through unobserved personal characteristics and not with causality.
Wolbachia Utilizes Host Microtubules and Dynein for Anterior Localization in the Drosophila Oocyte

To investigate the role of the host cytoskeleton in the maternal transmission of the endoparasitic bacteria Wolbachia, we have characterized their distribution in the female germ line of Drosophila melanogaster. In the germarium, Wolbachia are distributed to all germ cells of the cyst, establishing an early infection in the cell destined to become the oocyte. During mid-oogenesis, Wolbachia exhibit a distinct concentration between the anterior cortex and the nucleus in the oocyte, where many bacteria appear to contact the nuclear envelope. Following programmed rearrangement of the microtubule network, Wolbachia dissociate from this anterior position and become dispersed throughout the oocyte. This localization pattern is distinct from mitochondria and all known axis determinants. Manipulation of microtubules and cytoplasmic Dynein and Dynactin, but not Kinesin-1, disrupts anterior bacterial localization in the oocyte. In live egg chambers, Wolbachia exhibit movement in nurse cells but not in the oocyte, suggesting that the bacteria are anchored by host factors. In addition, we identify mid-oogenesis as a period in the life cycle of Wolbachia in which bacterial replication occurs. Total bacterial counts show that Wolbachia increase at a significantly higher rate in the oocyte than in the average nurse cell, and that normal Wolbachia levels in the oocyte depend on microtubules. These findings demonstrate that Wolbachia utilize the host microtubule network and associated proteins for their subcellular localization in the Drosophila oocyte. These interactions may also play a role in bacterial motility and replication, ultimately leading to the bacteria's efficient maternal transmission.
The DYPSA algorithm for estimation of glottal closure instants in voiced speech

We present the DYPSA algorithm for automatic and reliable estimation of glottal closure instants (GCIs) in voiced speech. Reliable GCI estimation is essential for closed-phase speech analysis, from which can be derived features of the vocal tract and, separately, the voice source. It has been shown that such features can be used with significant advantages in applications such as speaker recognition. DYPSA is automatic and operates using the speech signal alone without the need for an EGG or Laryngograph signal. It incorporates a new technique for estimating GCI candidates and employs dynamic programming to select the most likely candidates according to a defined cost function. We review and evaluate three existing methods and compare our new algorithm to them. Results for DYPSA show GCI detection accuracy to within ±0.25ms on 87% of the test database and fewer than 1% false alarms and misses.
Short-circuited series stubs for application in uniplanar low-pass filters

An alternative uniplanar low-pass filter with series stubs is presented in this paper and its upper stopband is extended up to five times of its cutoff frequency. The basic filter structure primarily consists of short-circuited series stubs on slot line and connecting lines on coplanar waveguide. Under the target of Chebyshev function low-pass frequency responses, all the element values involved in this filter topology is determined via efficient synthesis design approach rather try-to-cut optimization approach. Later on, the connecting line between adjacent stubs is replaced by its equivalent T-shaped transmission line to suppress the higher order harmonic bands. As design examples, two five-pole uniplanar filters with and without harmonic-suppressed elements embedded are designed, fabricated and measured.
Probabilistic Coherence Weighting for Optimizing Expert Forecasts

Methods for eliciting and aggregating expert judgment are necessary when decision-relevant data are scarce. Such methods have been used for aggregating the judgments of a large, heterogeneous group of forecasters, as well as the multiple judgments produced from an individual forecaster. This paper addresses how multiple related individual forecasts can be used to improve aggregation of probabilities for a binary event across a set of forecasters. We extend previous efforts that use probabilistic incoherence of an individual forecaster's subjective probability judgments to weight and aggregate the judgments of multiple forecasters for the goal of increasing the accuracy of forecasts. With data from two studies, we describe an approach for eliciting extra probability judgments to (i) adjust the judgments of each individual forecaster, and (ii) assign weights to the judgments to aggregate over the entire set of forecasters. We show improvement of up to 30% over the established benchmark of a simple equal-weighted averaging of forecasts. We also describe how this method can be used to remedy the “fifty--fifty blip” that occurs when forecasters use the probability value of 0.5 to represent epistemic uncertainty.
A content-based music retrieval engine: JMIR-Mozart

The rapid increase of storage capacity has brought along large-scale multimedia databases. To access such databases, content-based retrieval methods are needed in order to avoid the burden of handcraft involved in building a query system working on metadata. The burgeoning demand for such methods can be seen, for instance, in the number of researchers working on developing tools and algorithms to this end. In this paper, we present a prototypic, client-server query engine for content-based music retrieval (CBAAR). Our main aim is to help researchers working in the field so that they could have a retrieval platform where to embed and test their novel tools and algorithms without the burden of building a whole system from scratch. We give an overview to the platform: the architectural solutions, the communication protocols and user interface design. As for an example, we have embedded in this platform some music similarity and transcription algorithms developed in the C-BRAHMS research group, and thus achieved a complete retrieval system that can be queried on our website. We describe these algorithms in brief and discuss the performance of the retrieval system. The platform is released to public under the GNU General Public License, allowing anyone interested to freely use and modify the software.