Miracle-dz/UniFAR-FTUs huggingface dataset:
Foxc1 controls the growth of the murine frontal bone rudiment by direct regulation of a Bmp response threshold of Msx2

The mammalian skull vault consists of several intricately patterned bones that grow in close coordination. The growth of these bones depends on the precise regulation of the migration and differentiation of osteogenic cells from undifferentiated precursor cells located above the eye. Here, we demonstrate a role for Foxc1 in modulating the influence of Bmp signaling on the expression of Msx2 and the specification of these cells. Inactivation of Foxc1 results in a dramatic reduction in skull vault growth and causes an expansion of Msx2 expression and Bmp signaling into the area occupied by undifferentiated precursor cells. Foxc1 interacts directly with a Bmp responsive element in an enhancer upstream of Msx2, and acts to reduce the occupancy of P-Smad1/5/8. We propose that Foxc1 sets a threshold for the Bmp-dependent activation of Msx2, thus controlling the differentiation of osteogenic precursor cells and the rate and pattern of calvarial bone development.
Multi-level recovery

Multi-level transactions have received considerable attention as a framework for high-performance concurrency control methods. An inherent property of multi-level transactions is the need for compensating actions, since state-based recovery methods do no longer work correctly for transaction undo. The resulting requirement of operation logging adds to the complexity of crash recovery. In addition, multi-level recovery algorithms have to take into account that high-level actions are not necessarily atomic, e.g., if multiple pages are updated in a single action. In this paper, we present a recovery algorithm for multi-level transactions. Unlike typical commercial database systems, we have striven for simplicity rather than employing special tricks. It is important to note, though, that simplicity is not achieved at the expense of performance. We show how a high-performance multi-level recovery algorithm can be systematically developed based on few fundamental principles. The presented algorithm has been implemented in the DASDBS database kernel system.
Value of Tropheryma whipplei quantitative polymerase chain reaction assay for the diagnosis of Whipple disease: usefulness of saliva and stool specimens for first-line screening.

BACKGROUND Whipple disease (WD) is a chronic infectious disease caused by Tropheryma whipplei. WD DNA has been found in stool and saliva specimens from patients and asymptomatic carriers. METHODS A total of 4418 samples that were sent to our center for determination of WD were tested by a T. whipplei-specific quantitative polymerase chain reaction (PCR) based on repetitive sequences. Definite WD was diagnosed in 71 patients, including 55 patients with classic WD (defined by positive results of periodic acid-Schiff staining and/or specific immunohistochemistry of small-bowel biopsy specimens) and 16 patients with localized WD (including patients with endocarditis, neurologic infection, and uveitis). RESULTS Of the persons without WD, 2.3% had stool specimens positive for T. whipplei by PCR and 0.2% had saliva specimens positive for T. whipplei by PCR. Diagnosis of WD was likely in patients with positive results of both PCR of saliva specimens and PCR of stool specimens (positive predictive value, 95.2%). When the bacterial load was >10(4) colony-forming units per g of stool, the positive predictive value was 100%. A negative result of PCR of a saliva or stool specimen had a negative predictive value of 99.2% for classic WD. For localized WD, positive results of both PCR of saliva specimens and PCR of stool specimens had a sensitivity of 58% (compared with 94% for classic WD). The positive predictive value of testing of blood, cerebrospinal fluid, and urine specimens was 100% for each, and the positive predictive value for testing of duodenal biopsy specimens was 97.5%. CONCLUSIONS T. whipplei-specific quantitative PCR of saliva and stool specimens should be performed as first-line noninvasive screening for WD. When the results for both types of specimens are positive, diagnosis of classic WD should be highly suspected, especially if a high bacterial load is detected. Because PCR of saliva and stool specimens lacks sensitivity for determination of localized WD, invasive samples should be tested on the basis of clinical manifestations.
Bioavailability of iron to Trichodesmium colonies in the western subtropical Atlantic Ocean

Trichodesmium provides new nitrogen (N) to marine surface waters via N2 fixation, a process that requires a substantial amount of iron (Fe). Organic ligands in seawater that bind Fe could either increase or reduce the bioavailability of Fe. Electrochemical techniques indicate that these naturally occurring ligands have Fe‐binding constants similar to those of siderophores and porphyrins, suggesting that these chelators play an important role in determining the bioavailability of Fe to cyanobacteria. We conducted Fe uptake experiments using model ligands labeled with 55Fe to compare the bioavailability of inorganic Fe(III), porphyrin‐bound Fe(III), and siderophorebound Fe(III) to field‐collected Trichodesmium colonies. Inorganic Fe(III) and siderophore‐bound Fe(III) were more bioavailable to Trichodesmium colonies than was porphyrin‐bound Fe(III). Furthermore, the bioavailability of the siderophore‐bound Fe(III) can be characterized by the functional groups of the siderophore. The dihydroxamate siderophore and an uncharacterized ligand from a cultured Synechococcus sp. increased the bioavailability of Fe compared to the trihydroxamate siderophores. Except for experiments with desferrioxamine B, dark incubations resulted in lower Fe uptake rates for all treatments, relative to parallel lighted incubations. This suggests that light enhances the photochemical dissociation of most of the ligand complexes or that light energy is required for the active transport of Fe complexed to the model ligands. The Fe uptake rate of Trichodesmium colonies also differed slightly on the basis of colony morphology, with higher uptake rates with “puffs” than “tufts. ” These experiments show that Trichodesmium colonies are capable of discriminating between Fe bound to different organic complexes.
Toward Practical Definitions of Quality for Food Science

A new practical approach to developing workable definitions of quality is presented to overcome the numerous semantic and conceptual difficulties that are common with the use of the word quality in food science. This approach links the concept of quality, through a general definition, by adding the missing link of specific definitions related to measurable attributes and properties determined by standard methods to provide values that can be used to evaluate foods or to set specifications. It is compatible with control, assurance, HACCP, regulatory, TQM, and other normal uses of the both the word quality, and the concept quality, in food science and technology.
ON THE ‘ HOCKEY STICK ’ GLOBAL CLIMATE RECONSTRUCTION 2 EXECUTIVE

The Chairman of the Committee on Energy and Commerce as well as the Chairman of the Subcommittee on Oversight and Investigations have been interested in an independent verification of the critiques of Mann et al. (1998, 1999) [MBH98, MBH99] by McIntyre and McKitrick (2003, 2005a, 2005b) [MM03, MM05a, MM05b] as well as the related implications in the assessment. The conclusions from MBH98, MBH99 were featured in the Intergovernmental Panel on Climate Change report entitled Climate Change 2001: The Scientific Basis. This report concerns the rise in global temperatures, specifically during the 1990s. The MBH98 and MBH99 papers are focused on paleoclimate temperature reconstruction and conclusions therein focus on what appear to be a rapid rise in global temperature during the 1990s when compared with temperatures of the previous millennium. These conclusions generated a highly polarized debate over the policy implications of MBH98, MBH99 for the nature of global climate change, and whether or not anthropogenic actions are the source. This committee, composed of Edward J. Wegman (George Mason University), David W. Scott (Rice University), and Yasmin H. Said (The Johns Hopkins University), has reviewed the work of both articles, as well as a network of journal articles that are related either by authors or subject matter, and has come to several conclusions and recommendations. This Ad Hoc Committee has worked pro bono, has received no compensation, and has no financial interest in the outcome of the report.
C-Reactive Protein and B-Type Natriuretic Peptide Yield Either a Non-Significant or a Modest Incremental Value to Traditional Risk Factors in Predicting Long-Term Overall Mortality in Older Adults

Background New biomarkers may aid in preventive and end-of-life decisions in older adults if they enhance the prognostic ability of traditional risk factors. We investigated whether C-reactive protein (CRP) and/or B-type natriuretic peptide (BNP) improve the ability to predict overall mortality among the elderly of the Bambuí, Brazil Study of Aging when added to traditional risk factors. Methods From 1997 to 2007, 1,470 community-dwelling individuals (≥60 years) were followed-up. Death was ascertained by continuous verification of death certificates. We calculated hazard ratios per 1 standard deviation change (HR) of death for traditional risk factors only (old model), and traditional risk factors plus CRP and/or BNP (new models) and assessed calibration of the models. Subsequently, we compared c-statistic of each of the new models to the old one, and calculated integrated discriminative improvement (IDI) and net reclassification improvement (NRI). Results 544 (37.0%) participants died in a mean follow-up time of 9.0 years. CRP (HR 1.28, 95% CI 1.17-1.40), BNP (HR 1.31 95% CI 1.19-1.45), and CRP plus BNP (HR 1.26, 95% CI 1.15-1.38, and HR 1.29, 95% CI 1.16-1.42, respectively) were independent determinants of mortality. All models were well-calibrated. Discrimination was similar among the old (c-statistic 0.78 [0.78-0.81]) and new models (p=0.43 for CRP; p=0.57 for BNP; and p=0.31 for CRP plus BNP). Compared to the old model, CRP, BNP, and CRP plus BNP models led to an IDI of 0.009 (p<0.001), -0.005 (p<0.001) and -0.003 (p=0.84), and a NRI of 0.04 (p=0.24), 0.07 (p=0.08) and 0.06 (p=0.10), respectively. Conclusions Despite being independent predictors of long-term risk of death, compared to traditional risk factors CRP and/or BNP led to either a modest or non-significant improvement in the ability of predicting all-cause mortality in older adults.
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Analysis of the interaction between practices for introducing XP effectively

In this paper, we discuss interactions between XP (eXtreme Programming) practices. We discuss 2 case studies of introducing XP practices selectively from the 13 practices which are defined in XP, and we analyze how to select practices. Our analysis is based on interviews with developers. While it is difficult to introduce all the XP practices at once, our knowledge makes it easier to determine more effective combinations of practices.
Real-time rail-track monitoring system employing innovative wavelength diversity technique in distributed optical fibre sensors

Brillouin based distributed fibre sensors gained a lot of attention in recent years for structural health monitoring applications, due to their higher sensing range over tens of kilometres and distributed measurement capability of simultaneous strain and temperature. In Brillouin optical time domain reflectometry (BOTDR) system, the signal-to-noise ratio (SNR) determines the sensing performance of the system. However, the SNR is limited by the restricted maximum input pump power, which is limited by the non-negligible nonlinear effects, such as stimulated Brillouin scattering. In this research, a novel wavelength diversity technique is proposed to enhance the SNR, hence improve the strain and temperature measurement accuracies, which is required for accurate rail-track condition monitoring. In addition, this research work presents the following contributions (i) a simple, low-cost passive depolarizer is adopted to reduce the polarization noise; (ii) an inline erbium-doped fibre amplifier (EDFA) is employed at a certain distance to amplify the attenuated pulse in order to improve the sensing range; and (iii) a cost-effective reference Brillouin ring laser is used in BOTDR system to overcome the complexity of the receiver bandwidth reduction. The proposed wavelength diversity BOTDR system combined with a passive depolarizer and Brillouin ring laser is validated over a 50 km sensing fibre with a 5 m spatial resolution. The SNR is improved by 5.1 dB, which corresponds to 180% improvement compared to a conventional BOTDR system. Whereas, the strain and temperature accuracies at a 50 km fibre distance are ±10 μe and ±0.45oC, respectively. Furthermore, for the first time, simultaneous integration of long-term evolution (LTE) radio-over-fibre (RoF) data system and BOTDR sensing system using a single optical fibre is proposed and demonstrated. The error vector magnitude (EVM) performance of LTE-RoF data system is analysed for three modulation formats of QPSK, 16-QAM and 64-QAM in the presence of various BOTDR sensing powers.
Molecular Systems Biology Peer Review Process File Increasing Population Growth by Asymmetric Segregation of a Limiting Resource during Cell Division Transaction Report

(Note: With the exception of the correction of typographical or spelling errors that could be a source of ambiguity, letters and reports are not edited. The original formatting of letters and referee reports may not be reflected in this compilation.) Thank you again for submitting your work to Molecular Systems Biology. We have now heard back from the three referees who agreed to evaluate your manuscript. As you will see from the reports below, the referees find the topic of your study of potential interest. They raise, however, substantial concerns on your work, which, I am afraid to say, must preclude its publication in its present form. The reviewers each recognized that the mother-only proliferation pattern observed in this work was intriguing. However, each also raised important concerns which will need to be conclusively addressed before this work would be suitable for publication. The editor would like to emphasize that some of these issues appear to require substantial additional experiment work to address. The concerns raised by Reviewer #2, in particular, seem to indicate that some of the central time microscopy experiments need to be repeated with a more controlled transition from high-zinc to low-zinc growth media, to assure that other media differences are not contributing to the observed proliferation pattern. Moreover, this reviewer also felt that zinc limitation as the causative agent behind this growth pattern should more directly demonstrated, and these concerns seem to fall somewhat in line with comments from Reviewer #3. Lastly, the reviewers felt that the modeling component of this work should be incorporated more directly into the Results section, and Reviewer #1 had some important concerns with the formulation of these models. In addition, when preparing your revised manuscript, we ask that you consider supplying "source data" files for the Figures presented in this work, where applicable. In general, Molecular Systems Biology asks that authors supply the underlying numeric data for new experimental results. Figure source data is a new feature that allows these supplemental data to be more directly incorporated
Effect of CSA Concentration on the Ammonia Sensing Properties of CSA-Doped PA6/PANI Composite Nanofibers

Camphor sulfonic acid (CSA)-doped polyamide 6/polyaniline (PA6/PANI) composite nanofibers were fabricated using in situ polymerization of aniline under different CSA concentrations (0.02, 0.04, 0.06, 0.08 and 0.10 M) with electrospun PA6 nanofibers as templates. The structural, morphological and ammonia sensing properties of the prepared composite nanofibers were studied using scanning electron microscopy (SEM), Fourier transform infrared spectroscopy (FT-IR), four-point probe techniques, X-ray diffraction (XRD) and a home-made gas sensing test system. All the results indicated that the CSA concentration had a great influence on the sensing properties of CSA-doped PA6/PANI composite nanofibers. The composite nanofibers doped with 0.02 M CSA showed the best ammonia sensing properties, with a significant sensitivity toward ammonia (NH3) at room temperature, superior to that of the composite nanofibers doped with 0.04–0.10 mol/L CSA. It was found that for high concentrations of CSA, the number of PANI–H+ reacted with NH3 would not make up a high proportion of all PANI–H+ within certain limits. As a result, within a certain range even though higher CSA-doped PA6/PANI nanofibers had better conductivity, their ammonia sensing performance would degrade.
Rapid High Quality Compression of Volume Data for Visualization

Volume data sets resulting from, e.g., computerized tomography (CT) or magnetic resonance (MR) imaging modalities require enormous storage capacity even at moderate resolution levels. Such large files may require compression for processing in CPU memory which, however, comes at the cost of decoding times and some loss in reconstruction quality with respect to the original data. For many typical volume visualization applications (rendering of volume slices, subvolumes of interest, or isosurfaces) only a part of the volume data needs to be decoded. Thus, efficient compression techniques are needed that provide random access and rapid decompression of arbitrary parts the volume data. We propose a technique which is block based and operates in the wavelet transformed domain. We report performance results which compare favorably with previously published methods yielding large reconstruction quality gains from about 6 to 12 dB in PSNR for a5123 ‐volume extracted from the Visible Human data set. In terms of compression our algorithm compressed the data 6 times as much as the previous state‐of‐the‐art block based coder for a given PSNR quality.
Poly(ADP-ribose) Polymerase (PARP-1) in Homologous Recombination and as a Target for Cancer Therapy

Poly(ADP-ribose) polymerase (PARP-1) binds to DNA breaks to facilitate DNA repair. However, the role of PARP-1 in DNA repair appears to not be critical since PARP-1 knockout mice are viable, fertile and do not develop early onset tumours. Cells isolated from these mice show an increased level of homologous recombination. There is an intricate link between homologous recombination and PARP-1 and a possible role for PARP-1 in DNA double-strand break repair. Although PARP-1 appears not to be required for homologous recombination itself, it regulates the process through its involvement in the repair of DNA single-strand breaks (SSBs). SSBs persisting into the S phase of the cell cycle collapse replication forks, triggering homologous recombination for replication restart. We discuss the recent discoveries on the use of PARP-1 inhibitors as a targeted cancer therapy for recombination deficient cancers, such as BRCA2 tumours.
Revealing Online Learning Behaviors and Activity Patterns and Making Predictions with Data Mining Techniques in Online Teaching

This study was conducted with data mining (DM) techniques to analyze various patterns of online learning behaviors, and to make predictions on learning outcomes. Statistical models and machine learning DM techniques were conducted to analyze 17,934 server logs to investigate 98 undergraduate students’ learning behaviors in an online business course in Taiwan. The study scientifically identified students’ behavioral patterns and preferences in the online learning processes, differentiated active and passive learners, and found important parameters for performance prediction. The results also demonstrated how data mining techniques might be utilized to help improve online teaching and learning with suggestions for online instructors, instructional designers and courseware developers.
New insights into pacemaker activity: promoting understanding of sick sinus syndrome.

Sick sinus syndrome is an abnormality involving the generation of the action potential by the sinus node and is characterized by an atrial rate inappropriate for physiological requirements. Manifestations include severe sinus bradycardia, sinus pauses or arrest, sinus node exit block, chronic atrial tachyarrhythmias, alternating periods of atrial bradyarrhythmias and tachyarrhythmias, and inappropriate responses of heart rate during exercise or stress.1 Although its incidence increases in an exponential-like manner with age,1 it can occur at all ages, including in the newborn.2 The mean age of patients with the syndrome is 68 years, with both genders being affected in approximately equal proportion.2 The syndrome occurs in 1 of every 600 cardiac patients older than 65 years and accounts for approximately half of implantations of pacemakers in the United States.2 The syndrome is a collection of conditions, with a variety of causes intrinsic or extrinsic relative to the node.2 Age-dependent degenerative fibrosis of the tissues of the node has been suggested to be a common cause,2 although this is disputed.1 Clinical aspects of the syndrome have been reviewed many times.1–3 In this review, coinciding with the centenary of the discovery of the node, we offer new insights into intrinsic causes that come from an understanding of the mechanisms underlying pacemaking. It is now exactly 100 years since Arthur Keith (Figure 1A) performed the work that introduced the world to the location of the sinus node.4,5 Keith had been intrigued by the actions of the musculature of the heart and was anxious to establish any muscular mechanisms involved in closure of the great caval veins as the right atrium contracted to deliver its load to the ventricles.5 He was aware of the work of James Mackenzie, then a medical practitioner working …