Miracle-dz/UniFAR-FTUs huggingface dataset:
Molecular and Culture-Based Bronchoalveolar Lavage Fluid Testing for the Diagnosis of Cytomegalovirus Pneumonitis

Background. Cytomegalovirus (CMV) is a major cause of morbidity and mortality in immunocompromised patients, with CMV pneumonitis among the most severe manifestations of infection. Although bronchoalveolar lavage (BAL) samples are frequently tested for CMV, the clinical utility of such testing remains uncertain. Methods. Retrospective analysis of adult patients undergoing BAL testing via CMV polymerase chain reaction (PCR), shell vial culture, and conventional viral culture between August 2008 and May 2011 was performed. Cytomegalovirus diagnostic methods were compared with a comprehensive definition of CMV pneumonitis that takes into account signs and symptoms, underlying host immunodeficiency, radiographic findings, and laboratory results. Results. Seven hundred five patients underwent 1077 bronchoscopy episodes with 1090 BAL specimens sent for CMV testing. Cytomegalovirus-positive patients were more likely to be hematopoietic cell transplant recipients (26% vs 8%, P < .0001) and less likely to have an underlying condition not typically associated with lung disease (3% vs 20%, P < .0001). Histopathology was performed in only 17.3% of CMV-positive bronchoscopy episodes. When CMV diagnostic methods were evaluated against the comprehensive definition, the sensitivity and specificity of PCR, shell vial culture, and conventional culture were 91.3% and 94.6%, 54.4% and 97.4%, and 28.3% and 96.5%, respectively. Compared with culture, PCR provided significantly higher sensitivity and negative predictive value (P ≤ .001), without significantly lower positive predictive value. Cytomegalovirus quantitation did not improve test performance, resulting in a receiver operating characteristic curve with an area under the curve of 0.53. Conclusions. Cytomegalovirus PCR combined with a comprehensive clinical definition provides a pragmatic approach for the diagnosis of CMV pneumonitis.
Allelic variants of the amylose extender mutation of maize demonstrate phenotypic variation in starch structure resulting from modified protein–protein interactions

amylose extender (ae−) starches characteristically have modified starch granule morphology resulting from amylopectin with reduced branch frequency and longer glucan chains in clusters, caused by the loss of activity of the major starch branching enzyme (SBE), which in maize endosperm is SBEIIb. A recent study with ae− maize lacking the SBEIIb protein (termed ae1.1 herein) showed that novel protein–protein interactions between enzymes of starch biosynthesis in the amyloplast could explain the starch phenotype of the ae1.1 mutant. The present study examined an allelic variant of the ae− mutation, ae1.2, which expresses a catalytically inactive form of SBEIIb. The catalytically inactive SBEIIb in ae1.2 lacks a 28 amino acid peptide (Val272–Pro299) and is unable to bind to amylopectin. Analysis of starch from ae1.2 revealed altered granule morphology and physicochemical characteristics distinct from those of the ae1.1 mutant as well as the wild-type, including altered apparent amylose content and gelatinization properties. Starch from ae1.2 had fewer intermediate length glucan chains (degree of polymerization 16–20) than ae1.1. Biochemical analysis of ae1.2 showed that there were differences in the organization and assembly of protein complexes of starch biosynthetic enzymes in comparison with ae1.1 (and wild-type) amyloplasts, which were also reflected in the composition of starch granule-bound proteins. The formation of stromal protein complexes in the wild-type and ae1.2 was strongly enhanced by ATP, and broken by phosphatase treatment, indicating a role for protein phosphorylation in their assembly. Labelling experiments with [γ-32P]ATP showed that the inactive form of SBEIIb in ae1.2 was phosphorylated, both in the monomeric form and in association with starch synthase isoforms. Although the inactive SBEIIb was unable to bind starch directly, it was strongly associated with the starch granule, reinforcing the conclusion that its presence in the granules is a result of physical association with other enzymes of starch synthesis. In addition, an Mn2+-based affinity ligand, specific for phosphoproteins, was used to show that the granule-bound forms of SBEIIb in the wild-type and ae1.2 were phosphorylated, as was the granule-bound form of SBEI found in ae1.2 starch. The data strongly support the hypothesis that the complement of heteromeric complexes of proteins involved in amylopectin synthesis contributes to the fine structure and architecture of the starch granule.
On the Distribution of Mutant Characters among the Chromosomes of OENOTHERA LAMARCKIANA.

During the last ten years the number of distinct mutant types of Oenothera Lamarckiana has increased considerably. One of us has determined the chromosome numbers for most of them, including those older ones, for which these figures had not as yet been ascertained. Moreover the fact that some mutant types are repeatedly produced by others has become very prominent, indicating some kind of genetic relationship. Outward features are often observed to run parallel with such connections; in other cases they are so much alike, as to give another trustworthy basis for the assumption of closer relations. Starting from these facts, we have tried to arrange the mutant types into distinct groups, analogous to those proposed by MORGAN and his disciples for Drosophila. Unfortunately, it is in our case mostly impossible to determine dihybrid splitting figures, such as constitute the basis for MORGAN'S deductions. Differences in the ratio of growth of the pollen tubes, preferential fertilkation of one of the kinds of egg-cells, in those cases where there are two or more of them, deviations in the partial sterility of pollen-grains and of seeds are among the main causes which tend to discard numerical data from our present considerations. But the distinctness of our results does not seem to suffer from this difficulty. We start from the numbers of the chromosomes, and bring those mutants, which do not deviate in this respect from the main species, into our first group. In doing so, we find that almost all of them belong to the ordinary types of mutations. They are mostly due to recessive characters, as, for instance, the dwarfs and the brittle races. In a large number 'of the other mutants one of the chromosomes is doubled, bringing the total number of these bodies up from seven to eight
Implicit scene modelling from imprecise point clouds

In applying optical methods for automated 3D indoor modelling, the 3D reconstruction of objects and surfaces is very sensitive to both lighting conditions and the observed surface properties, which ultimately compromise the utility of the acquired 3D point clouds. This paper presents a robust scene reconstruction method which is predicated upon the observation that most objects contain only a small set of primitives. The approach combines sparse approximation techniques from the compressive sensing domain with surface rendering approaches from computer graphics. The amalgamation of these techniques allows a scene to be represented by a small set of geometric primitives and to generate perceptually appealing results. The resulting scene surface models are defined as implicit functions and may be processed using conventional rendering algorithms such as marching cubes, to deliver polygonal models of arbitrary resolution. It will also be shown that 3D point clouds with outliers, strong noise and varying sampling density can be reliably processed without manual intervention.
An efficient quantization algorithm for solving average-consensus problems

In this work we present a new algorithm to solve the average-consensus problem. The main goal of this algorithm is to obtain exact convergence despite the existence of quantized communication channels between the agents. Starting from the Zoom-in Zoom-out strategy already presented in [5], we introduce the equations describing the behaviour of the algorithm and we formally prove the asymptotic agreement. We will also show that, under a reasonable hypothesis, the algorithm parameters ensuring convergence, can be chosen regardless the number of agents.
The Good, the Bad and the Ambiguous: Standards and Trade in Agricultural Products

Do countries use standards to protect their agricultural sectors from imports? This question has taken center stage in the agricultural trade-policy debate for years. This paper empirically evaluates three commonly made claims: (1) country-specific agricultural standards uniformly hinder trade, (2) harmonization of standards uniformly promotes trade in agricultural goods and (3) within tradeblocks, both harmonized and country-specific standards have a different effect on insiders than on outsiders. We argue that these claims ignore important economic trade-offs: Country-specific standards hinder trade, since they enforce costly testing or adaptation of products, but they also provide essential information about markets. Harmonization of standards eliminates product adaptation costs, but also reduces variety, thus reducing trade. Trade blocks form coalitions that allow choosing optimally which standards to harmonize and which ones to leave as country-specific. Outsiders are therefore harder hit by country-specific standards than insiders. If outsiders of a tradeblock harmonize their standards with those of insiders, they benefit from increased trade with them. Not surprisingly, we only find partial evidence for the first two, but strong evidence for the third claim.
Cross Language Information Retrieval : an Experiment in Bilingual News Article Alignment from the Internet using MT

Cross Language Information Retrieval (CLIR) o ers the potential for users to search document collections in foreign languages. This is particularly relevant now that the Internet has become a global information source. Machine translation (MT) has a key role in bridging the gap between the language of the users' query and that of the document collection as well as to help the user understand the search results with gisting. In this paper we reformulate the CLIR task as text alignment on a database of Reuter news articles. We show preliminary results for CLIR using relevance feedback with machine-translated queries from Japanese into English.
Preventable in-hospital medical injury under the “no fault” system in New Zealand

Objectives: To describe the pattern of preventable in-hospital medical injury under the “no fault” system and to assess the level of serious preventable patient harm. Design: Cross sectional survey using a two stage retrospective assessment of medical records conducted by structured implicit review. Setting: General hospitals with over 100 beds providing acute care in New Zealand. Participants: A sample of 6579 patients admitted in 1998 to 13 hospitals selected by stratified systematic list sample. Main outcome measures: Occurrence, preventability, and impact of adverse events. Results: Over 5% of admissions were associated with a preventable in-hospital event, of which nearly half had an element of systems failure. The elderly, ethnic minority groups, and particular clinical areas were at higher risk. The chances of a patient experiencing a serious preventable adverse event subsequent to hospital admission were just under 1%, a figure close to published results from comparable studies under tort. On average, these events required an additional 4 weeks in hospital. System related issues of protocol use and development, communication, and organisation, as well as requirements for consultation and education, were pre-eminent. Conclusions: The risk of serious preventable in-hospital medical injury for patients in New Zealand, a well established “no fault” jurisdiction, is within the range reported in comparable investigations under tort.
Breakdown Voltage for Superjunction Power Devices With Charge Imbalance: An Analytical Model Valid for Both Punch Through and Non Punch Through Devices

An analytical model for the electric field and the breakdown voltage (BV) of an unbalanced superjunction (SJ) device is presented in this paper. The analytical technique uses a superposition approach treating the asymmetric charge in the pillars as an excess charge component superimposed on a balanced charge component. The proposed double-exponential model is able to accurately predict the electric field and the BV for unbalanced SJ devices in both punch through and non punch through conditions. The model is also reasonably accurate at extremely high levels of charge imbalance when the devices behave similarly to a PiN diode or to a high-conductance layer. The analytical model is compared against numerical simulations of charge unbalanced SJ devices and against experimental results.
Understanding the limitations of radiation-induced cell cycle checkpoints

The DNA damage response pathways involve processes of double-strand break (DSB) repair and cell cycle checkpoint control to prevent or limit entry into S phase or mitosis in the presence of unrepaired damage. Checkpoints can function to permanently remove damaged cells from the actively proliferating population but can also halt the cell cycle temporarily to provide time for the repair of DSBs. Although efficient in their ability to limit genomic instability, checkpoints are not foolproof but carry inherent limitations. Recent work has demonstrated that the G1/S checkpoint is slowly activated and allows cells to enter S phase in the presence of unrepaired DSBs for about 4–6 h post irradiation. During this time, only a slowing but not abolition of S-phase entry is observed. The G2/M checkpoint, in contrast, is quickly activated but only responds to a level of 10–20 DSBs such that cells with a low number of DSBs do not initiate the checkpoint or terminate arrest before repair is complete. Here, we discuss the limitations of these checkpoints in the context of the current knowledge of the factors involved. We suggest that the time needed to fully activate G1/S arrest reflects the existence of a restriction point in G1-phase progression. This point has previously been defined as the point when mitogen starvation fails to prevent cells from entering S phase. However, cells that passed the restriction point can respond to DSBs, albeit with reduced efficiency.
Cosmetic Analysis Using Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry Imaging (MALDI-MSI)

A new “omic” platform—Cosmetomics—that proves to be extremely simple and effective in terms of sample preparation and readiness for data acquisition/interpretation is presented. This novel approach employing Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry Imaging (MALDI-MSI) for cosmetic analysis has proven to readily identify and quantify compounds of interest. It also allows full control of all the production phases, as well as of the final product, by integration of both analytical and statistical data. This work has focused on products of daily use, namely nail polish, lipsticks and eyeliners of multiple brands sold in the worldwide market.
Draft Genome Sequence of Olsenella scatoligenes SK9K4T, a Producer of 3-Methylindole (Skatole) and 4-Methylphenol (p-Cresol), Isolated from Pig Feces

ABSTRACT Olsenella scatoligenes SK9K4T is a strictly anaerobic bacterium isolated from pig feces that produces the malodorous compounds 3-methylindole (skatole) and 4-methylphenol (p-cresol). Here, we report the 2.47 Mbp draft genome sequence of SK9K4T, exploring pathways for the synthesis of skatole and p-cresol from the amino acids tryptophan and tyrosine, respectively.
Relevant image pre-filtering in automatic image orientation correction

In this paper, we propose a method for improving automatic image orientation correction by relevant image pre-filtering. We find out that users feel more stress on false positives than false negatives in automatic correction through a user study. A strategy based on this finding is devised and our method realizes this strategy by filtering out irrelevant images which are likely to become false positives. The accuracy evaluations with actual personal photos show improvements of the precision from 94% to 98% at the recall ratio of 15%, and from 97.5% to 100% at the recall ratio of 10%. A subjective survey concludes the proposed pre-filtering alleviates the users' annoyance for automatic orientation corrections.
Data on Air: Organization and Access

Organizing massive amount of data on wireless communication networks in order to provide fast and low power access to users equipped with palmtops, is a new challenge to the data management and telecommunication communities. Solutions must take under consideration the physical restrictions of low network bandwidth and limited battery life of palmtops. This paper proposes algorithms for multiplexing clustering and nonclustering indexes along with data on wireless networks. The power consumption and the latency for obtaining the required data are considered as the two basic performance criteria for all algorithms. First, this paper describes two algorithms namely, (1, m) indexing and Distributed Indexing, for multiplexing data and its clustering index. Second, an algorithm called Nonclustered Indexing is described for allocating static data and its corresponding nonclustered index. Then, the Nonclustered indexing algorithm is generalized to the case of multiple indexes. Finally, the proposed algorithms are analytically demonstrated to lead to significant improvement of battery life while retaining a low latency.
Differential interferometry techniques on l-band data employed for the monitoring of surface subsidence due to mining

Mining activities in South Africa changes the natural environment in several ways. Challenges for mining companies lie in the detection and monitoring of surface subsidence and there exists a need for a long term monitoring system. Field-based techniques for deformation measurement are labour intensive and time consuming and, consequently, the implementation of these techniques for long-term monitoring is not ideal. On the other hand, satellite remote sensing data provides a synoptic view of an area and the repeat image acquisition strategy implies that the long-term monitoring of surface deformation is a possibility. This paper investigates the use of L-band ALOS PALSAR data for the detection and monitoring of surface subsidence due to underground mining activities in the Witbank Coalfields. Surface subsidence was detected for a period of over 3 years between 2007/08/16 and 2010/10/09. Centimetre scale surface deformation was detected in the study area and is associated with areas of active mining. The systematic evolution of the surface deformation basins over time was recognised and is consistent with the advance of the working face of the mine during the same period. The results confirm that L-band synthetic aperture radar data through dInSAR techniques can be used for the long-term monitoring of surface subsidence associated with mining activities.
The Effects of Public School Choice on the Academic Achievement of Minority Students.

Black and Hispanic students are more likely to exercise public school choice. Previous large-scale quantitative studies have ignored ethnic distinctions as well as choice's multi-dimensional nature. As a result, the effects of public sector choice policy on the academic achievement of minority students are unknown. This study uses data from the National Educational Longitudinal Study of 1988 in a structural equation model to test and compare the effects of school choice on the academic achievement of 853 Black and Hispanic high school students. The authors conclude that school choice has no indirect effect on academic achievement. Other findings include; a student's socioeconomic status predicts choice, school choice positively influences a sense of belonging and support, and school choice's influence on student effort is indirectly transmitted via an enhanced sense of belonging and support. Finally, choosing does not increase the likelihood students will enroll in an academically rigorous program.
Crystal structures of N-(4-chlorophenyl)-2-[(4,6-diaminopyrimidin-2-yl)sulfanyl]acetamide and N-(3-chlorophenyl)-2-[(4,6-diaminopyrimidin-2-yl)sulfanyl]acetamide

The title compounds, (I) and (II), are 2-[(diaminopyrimidin-2-yl)sulfanyl]acetamides. The molecules have a folded conformation, with the pyrimidine ring being inclined to the benzene ring by 42.25 (14)° in (I), and by 59.70 (16) and 62.18 (15)° in the two independent molecules of compound (II).
Dividend Payout Policy and Life Cycle Theory: An Empirical Evidence from Istanbul Stock Exchange Manufacturing Firms

The paper tests the validty of life cycle theory of dividends in the Turkey by using the dataset of 146 ISE listed manufacturing firms for the period 2006-2011 and employing the logit and probit models. As a result we find the evidence supporting the life cycle theory of dividends in Turkey. In addition to this, firms with high profitability and cash ratio tend to pay more dividends. The findings have important implications for investors.
Time/area tradeoffs in testing hierarchical SOCs with hard mega-cores

Motivated by the presence of mega-cores in hierarchical systems-on-a-chip, This work describes a new framework for the design space exploration of multi-level test access mechanisms. Test resources are placed next to the mega-core wrappers, which removes the constraint that upper-level TAM width must be wider than the internal TAM width of the mega-core. The proposed solution can rapidly analyze the tradeoffs between test application time and area overhead and it facilitates test data reuse for hard mega-cores.
Auditory Steady State Cortical Responses Indicate Deviant Phonemic-Rate Processing in Adults With Dyslexia

Objectives: Speech intelligibility is strongly influenced by the ability to process temporal modulations. It is hypothesized that in dyslexia, deficient processing of rapidly changing auditory information underlies a deficient development of phonological representations, causing reading and spelling problems. Low-frequency modulations between 4 and 20 Hz correspond to the processing rate of important phonological segments (syllables and phonemes, respectively) in speech and therefore provide a bridge between low-level auditory and phonological processing. In the present study, temporal modulation processing was investigated by auditory steady state responses (ASSRs) in normal-reading and dyslexic adults. Design: Multichannel ASSRs were recorded in normal-reading and dyslexic adults in response to speech-weighted noise stimuli amplitude modulated at 80, 20, and 4 Hz. The 80 Hz modulation is known to be primarily generated by the brainstem, whereas the 20 and 4 Hz modulations are mainly generated in the cortex. Furthermore, the 20 and 4 Hz modulations provide an objective auditory performance measure related to phonemic- and syllabic-rate processing. In addition to neurophysiological measures, psychophysical tests of speech-in-noise perception and phonological awareness were assessed. Results: On the basis of response strength and phase coherence measures, normal-reading and dyslexic participants showed similar processing at the brainstem level. At the cortical level of the auditory system, dyslexic subjects demonstrated deviant phonemic-rate responses compared with normal readers, whereas no group differences were found for the syllabic rate. Furthermore, a relationship between phonemic-rate ASSRs and psychophysical tests of speech-in-noise perception and phonological awareness was obtained. Conclusions: The results suggest reduced cortical processing for phonemic-rate modulations in dyslexic adults, presumably resulting in limited integration of temporal information in the dorsal phonological pathway.