Miracle-dz/UniFAR-FTUs huggingface dataset:
Nucleic Acids Research

A picosecond UV laser was used to cross-link proteins to DNA in nuclei, whole cells and reconstituted nucleohistone. Irradiation of the nucleohistone resulted in crosslinking 15-20% of bound histones to DNA in a very short time (one or several picosecond pulses), the efficiency of crosslinking to single stranded DNA being higher than to double stranded DNA. All histones as well as high mobility group 1 proteins were identified in the covalently linked protein-DNA complexes upon irradiation of isolated nuclei and whole cells. A method is suggested for isolation of crosslinked material from cells and nuclei in amounts sufficient for further analysis. Experiments with reconstituted nucleohistones showed that upon irradiation at a constant dose the efficiency of crosslinking depended on the intensity of the light, thus suggesting a two-quantum process is involved in the reaction.
Rhythm Detection in Recorded Music

My research concerns rhythm detection in recorded music. Using the matrix mathematics system Matlab, we analyzed the rhythmic structure of several musical selections and compared the results to our musical analysis by ear. Rhythm is a low frequency component of music, in contrast to pitch, which is a high frequency component. Our first task was to filter out the high frequencies in order to study rhythm. Our data reduction algorithm separates recorded music into frequency bands, of roughly half an octave each, and extracts the energy in each band. Once this was done, the Discrete Fourier Transform can identify the primary rhythmic content of each band. We found that the time signatures of the pieces we analyzed were characterized by the rhythmic relationship between low and high frequency bands. We have written Matlab algorithms that implement these ideas.
Deep inferior epigastric perforator flap: An anatomical study of the perforators and local vascular differences

The objective of this study was to determine precise localization and external diameter of the lower abdominal wall perforators as well as to investigate some vascularity differences between the same parts of perfusion zones II and III according to Hartrampf perfusion zones. The study was performed on 10 fresh cadavers (20 hemiabdomens) using the gelatin injection technique. All perforators were identified, and their localization and diameter were noted. Measurements were made at the level of the fascia. We noted localization and diameter of arteries on cross‐sectional planes of either part of the flap. The median sum of the external diameter of all arteries in zone I was 17.01 mm. The median sum of the external diameter of all arteries in the medial 1/3 part of zone III was 4.17 mm, and in the medial 1/3 part of zone II, it was 0.96 mm. The median sum of the external diameter of all arteries in the intermediary 1/3 part of zone III was 2.16 mm, whereas in the intermediary 1/3 part of zone II, it was 0.81 mm. Significant differences were recorded between proximal and middle horizontal regions of zones II and III and between medial vertical part of zone III and medial vertical part of zone II. Anastomoses between zones I and II are considerably smaller compared with anastomoses between zones I and III. The best vascularized parts of the lower abdominal wall were perfusion zone I, then the inner 2/3 of zone III and medial 1/3 of zone II. © 2011 Wiley Periodicals, Inc. Microsurgery, 2012.
Global food demand and the sustainable intensification of agriculture

Global food demand is increasing rapidly, as are the environmental impacts of agricultural expansion. Here, we project global demand for crop production in 2050 and evaluate the environmental impacts of alternative ways that this demand might be met. We find that per capita demand for crops, when measured as caloric or protein content of all crops combined, has been a similarly increasing function of per capita real income since 1960. This relationship forecasts a 100–110% increase in global crop demand from 2005 to 2050. Quantitative assessments show that the environmental impacts of meeting this demand depend on how global agriculture expands. If current trends of greater agricultural intensification in richer nations and greater land clearing (extensification) in poorer nations were to continue, ∼1 billion ha of land would be cleared globally by 2050, with CO2-C equivalent greenhouse gas emissions reaching ∼3 Gt y−1 and N use ∼250 Mt y−1 by then. In contrast, if 2050 crop demand was met by moderate intensification focused on existing croplands of underyielding nations, adaptation and transfer of high-yielding technologies to these croplands, and global technological improvements, our analyses forecast land clearing of only ∼0.2 billion ha, greenhouse gas emissions of ∼1 Gt y−1, and global N use of ∼225 Mt y−1. Efficient management practices could substantially lower nitrogen use. Attainment of high yields on existing croplands of underyielding nations is of great importance if global crop demand is to be met with minimal environmental impacts.
Quantized CSI-Based Tomlinson-Harashima Precoding in Multiuser MIMO Systems

This paper considers the implementation of Tomlinson-Harashima (TH) precoding for multiuser MIMO systems based on quantized channel state information (CSI) at the transmitter side. Compared with the results in [1], our scheme applies to more general system setting where the number of users in the system can be less than or equal to the number of transmit antennas. We also study the achievable average sum rate of the proposed quantized CSI-based TH precoding scheme. The expressions of the upper bounds on both the average sum rate of the systems with quantized CSI and the mean loss in average sum rate due to CSI quantization are derived. We also present some numerical results. The results show that the nonlinear TH precoding can achieve much better performance than that of linear zero-forcing precoding for both perfect CSI and quantized CSI cases. In addition, our derived upper bound on the mean rate loss for TH precoding converges to the true rate loss faster than that of zero-forcing precoding obtained in [2] as the number of feedback bits becomes large. Both the analytical and numerical results show that nonlinear precoding suffers from imperfect CSI more than linear precoding does.
Effect of Aged Garlic Extract on the Cytotoxicity of Alzheimer β-Amyloid Peptide in Neuronal PC12 Cells

Alzheimer's disease (AD) is the most common cause of progressive intellectual failure and memory impairment among the elderly, affecting over 4 million Americans. A hallmark of the disease is the accumulation of β-amyloid, whose neurotoxicity has been well documented. A therapeutic approach may be to ameliorate this toxicity. Garlic has antioxidant, anti-aging and anti-ischemic properties. The purpose of the present study was to determine whether aged garlic extract attenuates the effect of neurotoxin, β-amyloid 25–35 (Aβ) in neuronal PC12 cells. Proliferating (non-neuronal) PC12 cells were treated with the nerve growth factor for at least 4 days before experiments were initiated. This treatment differentiates PC12 cells to a neuronal cell line. Cell viability was determined using the MTS-based assay (Promega). Wakunaga of America (Mission Viejo, CA) kindly donated aged garlic extractTM (AGETM) as KyolicR liquid. AGETM was sterilized by filtration and diluted in cell growth medium. Our results show that AGE™ protects neuronal PC12 cells against Aβ (95nM) toxicity in a dose dependent manner. AGETM may be effective in ameliorating Aβ -neurotoxicity.
Lessons from Chernobyl and prognosis for Fukushima: radiological consequences

The following are considered: results of large-scale radiation epidemiological studies of the health effects of the Chernobyl accident, radiation risks for emergency workers and the affected population; and verification of ICRP risk models taking into account data on the Chernobyl accident and preliminary prognostic estimates of potential radiological consequences of the Fukushima disaster.
MDCT for suspected appendicitis: effect of reconstruction section thickness on diagnostic accuracy, rate of appendiceal visualization, and reader confidence using axial images.

OBJECTIVE The purpose of this study was to evaluate interpretative performance with different MDCT reconstruction parameters in adult patients with suspected appendicitis. MATERIALS AND METHODS MDCT scans of 212 adult patients obtained in an emergency department with a 64-MDCT scanner were prospectively collected. Acquisition technique included 24 x 1.2 mm detector configuration and IV contrast administration with or without oral contrast administration. Data sets were reconstructed with three techniques: 5 x 5 mm, 3 x 3 mm, and 2 x 1 mm (section thickness x interval). Each of the 212 sets of images (grouped by reconstruction technique) was reviewed retrospectively using axial sections by two independent readers blinded to diagnosis. Medical record review was conducted to identify patients with appendicitis. Visualization of the appendix, confidence in visualization, confidence for presence or absence of specific CT findings, diagnostic accuracy, and diagnostic confidence were compared across reconstruction techniques. Data were analyzed with simple and ordinal logistic regression with adjustment for multiple observations derived from each patient and for reader differences. RESULTS Progressively thinner reconstruction section thickness was associated with a significant increase in the rate of visualization of the appendix (p < 0.001 for 5 x 5 vs 3 x 3; p = 0.03 for 3 x 3 vs 2 x 1), visualization confidence (p < 0.001 for 5 x 5 vs 3 x 3 and 3 x 3 vs 2 x 1), and confidence for presence or absence of findings. Seventeen subjects (8%) had appendicitis. Correctness of diagnosis was not significantly associated with reconstruction method. However, for correctly diagnosed cases interpreted as normal, impression confidence increased with progressively thinner section thickness (p < 0.001 for 5 x 5 vs 3 x 3 and 3 x 3 vs 2 x 1). CONCLUSION In this investigation of contrast-enhanced MDCT of the appendix, visual ization of the appendix and confidence in interpretation of axial images progressively improved with use of thinner reconstruction sections.
Case Report: Cerebrotendinous xanthomatosis

Cerebrotendinous xanthomatosis is a rare genetic disorder. We present and discuss the clinical, radiological, and histopathologic findings in a 36-year-old woman who had juvenile cataract, childhood diarrhea, mental retardation, cerebellar ataxia, and bilateral Achilles tendon xanthomas. She was thoroughly investigated radiologically and biopsy confirmed the diagnosis of xanthomas.
Complete Transcriptome of the Soybean Root Hair Cell, a Single-Cell Model, and Its Alteration in Response to Bradyrhizobium japonicum Infection1[C][W][OA]

Nodulation is the result of a mutualistic interaction between legumes and symbiotic soil bacteria (e.g. soybean [Glycine max] and Bradyrhizobium japonicum) initiated by the infection of plant root hair cells by the symbiont. Fewer than 20 plant genes involved in the nodulation process have been functionally characterized. Considering the complexity of the symbiosis, significantly more genes are likely involved. To identify genes involved in root hair cell infection, we performed a large-scale transcriptome analysis of B. japonicum-inoculated and mock-inoculated soybean root hairs using three different technologies: microarray hybridization, Illumina sequencing, and quantitative real-time reverse transcription-polymerase chain reaction. Together, a total of 1,973 soybean genes were differentially expressed with high significance during root hair infection, including orthologs of previously characterized root hair infection-related genes such as NFR5 and NIN. The regulation of 60 genes was confirmed by quantitative real-time reverse transcription-polymerase chain reaction. Our analysis also highlighted changes in the expression pattern of some homeologous and tandemly duplicated soybean genes, supporting their rapid specialization.
Mutations and polymorphisms in the proprotein convertase subtilisin kexin 9 (PCSK9) gene in cholesterol metabolism and disease

Hypercholesterolemia is one of the major causes of coronary heart disease (CHD). The genes encoding the low‐density lipoprotein receptor and its ligand apolipoprotein B, have been the two genes classically implicated in autosomal dominant hypercholesterolemia (ADH). Our discovery in 2003 of the first mutations of the proprotein convertase subtilisin kexin 9 gene (PCSK9) causing ADH shed light on an unknown actor in cholesterol metabolism that since then has been extensively investigated. Several PCSK9 variants have been identified, some of them are gain‐of‐function mutations causing hypercholesterolemia by a reduction of low‐density lipoprotein (LDL) receptor levels; while others are loss‐of‐function variants associated with a reduction of LDL‐cholesterol (LDL‐C) levels and a decreased risk of CHD. In this review, we focus on reported variants, and their biological, clinical, and functional relevance. We also highlight the spectrum of hypercholesterolemia or hypobetalipoproteinemia phenotypes that are already associated with mutations in PCSK9. Finally, we present future prospects concerning this therapeutic target that might constitute a new approach to reduce cholesterol levels and CHD, and enhance the effectiveness of other lipid‐lowering drugs. Hum Mutat 0, 1–11, 2008. © 2008 Wiley‐Liss, Inc.
Molecular dynamics of carboxymethyl κ/ι-hybrid carrageenan films doped with NH4I

ABSTRACT The effect of carboxymethylation and NH4I incorporation on the molecular dynamics of carrageenan films was studied. Broadband Dielectric Spectroscopy (BDS) assessed the presence of α and β relaxation processes. The effect of NH4I content was analyzed using the Havriliak-Negami model and parameterizing the temperature dependence of the relaxation times according to the Vogel-Fulcher-Tammann-Hesse (VFTH) equation. The glass transition temperature was found to decrease with the increase of NH4I content. These results suggest that carboxymethylation and the salt doping treatment increase the molecular mobility of NH4+ ions, making the films suitable for the development of solid electrolytes for energy storage applications. Graphical Abstract
Investigating Solution‐Phase Protein Structure and Dynamics by Hydrogen Exchange Mass Spectrometry

By taking advantage of labeling methods such as hydrogen exchange (HX), many details about protein conformation, dynamics, and interactions can be revealed by mass spectrometry. In this unit, hydrogen exchange theory is discussed as it applies to HX‐MS protocols, the practice of HX‐MS including data analysis and interpretation is explained in detail, and recent advancements in technology which greatly increase the depth of information gained from the technique are highlighted. Curr. Protoc. Protein Sci. 58:17.6. 1‐17.9. 17. © 2009 by John Wiley & Sons, Inc.
Tool Demo: Scala-Virtualized

This paper describes Scala-Virtualized, which extends the Scala language and compiler with a small number of features that enable combining the benefits of shallow and deep embeddings of DSLs. We demonstrate our approach by showing how to embed three different domain-specific languages in Scala. Moreover, we summarize how others have been using our extended compiler in their own research and teaching. Supporting artifacts of our tool include web-based tutorials, nightly builds, and an Eclipse update site hosting an up-to-date version of the Scala IDE for Eclipse based on the Virtualized Scala compiler and standard library.
Performance Analysis of Closed-Loop MIMO Precoder Based on the Probability of Minimum Distance

Linear closed-loop MIMO precoders are attractive owing to their scalability. They can significantly improve the received signal via optimization of pertinent criterion. The solution of max-dmin precoding is optimal for 4-QAM as it utilizes the channel state information at the transmitter (CSIT) to minimize the system error probability making it very attractive. However, as M increases the solution which is dependent on channel angle gets complex, due to its multi-form precoder search. Motivated by a requirement to provide MIMO system evaluation parameters to upper layer protocol(s) as a function of precoder optimization criterion, we propose deriving a general expression for the probability density function (pdf) of max-dmin. Our approach applies numerical approximations to derive the system bit error rate (BER) and ergodic capacity for any values of M, nr, and nt, and with b = 2 data streams. Results show that the performance of our numerical approximation approach is close to the analytical simulation method.
Characterization of the quality of the steamed yoghurts enriched by dates flesh and date powder variety H’loua

The purpose of the present work was to investigate the effect of including date flesh and date powder in the steamed yoghurt processing on some quality during four weeks of storage. In order to obtain the powders, date variety of H’loua was washed, cut into small particles, and then dried at 90 °C during 2 h. Seven steamed yoghurts were manufactured: control prepared by 80 g/L sucrose, yoghurts manufactured by replacement of some quantity of sucrose by 10, 20 and 25 g/L of the date powder and yoghurts prepared by replacement of some quantity of sucrose by 60, 70 and equal quantity 80 g/L of date flesh. All samples were analyzed for some physicochemical, biochemical, microbiological and sensory characteristics at 1, 7, 15, 21 and 29 days of storage. The total or partial replacement of the sucrose by date flesh and date powder improves the nutritional quality of the yoghurts such as proteins, fat, ash, and dry mater, but the level of the total sugars was decreased. Results of microbiological analyze showed complete absence of the total and fecal coliforms, Staphylococcus aureus, faecal streptococci and Salmonella in all yoghurts prepared and throughout the storage period. Replacement of the sucrose by all types of date improves the sensory characteristics of the yoghurts included taste and texture. Keyword: Date flesh, date powder, H’loua, Quality, Sucrose, Yoghurt.
The brain's specialized systems for aesthetic and perceptual judgment

We recorded brain activity when 21 subjects judged the beauty (aesthetic or affective judgment) and brightness (perceptual or cognitive judgment) of simultaneously presented paintings. Aesthetic judgments engaged medial and lateral subdivisions of the orbitofrontal cortex as well as subcortical stations associated with affective motor planning (globus pallidus, putamen–claustrum, amygdala, and cerebellar vermis), whereas the motor, premotor and supplementary motor areas, as well as the anterior insula and the dorsolateral prefrontal cortex, were engaged by both kinds of judgment. The results lead us to conclude: (i) that there is a functional specialization for judgment, with aesthetic judgments engaging distinct systems, in addition to those that they share with perceptual judgments; (ii) that the systems engaged by affective judgments are those in which activity correlates with polar experiences (e.g. love–hate, beauty–ugliness, and attraction–repulsion); and (iii) that there is also a functional specialization in the motor pathways, with aesthetic judgments engaging motor systems not engaged by perceptual judgments, in addition to those engaged by both kinds of judgment.
High Mixing Efficiency by Modulating Inlet Frequency of Viscoelastic Fluid in Simplified Pore Structure

Fluid mixing plays an essential role in microscale flow systems. Here, we propose an active mixing approach which enhances the mixing of viscoelastic fluid flow in a simplified pore T-junction structure. Mixing is actively controlled by modulating the driving pressure with a sinusoidal signal at the two inlets of the T-junction. The mixing effect is numerically investigated for both Newtonian and viscoelastic fluid flows under different pressure modulation conditions. The result shows that a degree of mixing as high as 0.9 is achieved in viscoelastic fluid flows through the T-junction mixer when the phase difference between the modulated pressures at the two inlets is 180°. This modulation method can also be used in other fluid mixing devices.
Data Set Selection for a Constrained Simple Sonification

Previous work on the production and test of various sonifications has shown that adding a sonification to an interface can assist the execution of a variety of operator tasks [1,2,3]. However, it has also shown that in some cases sonifications can have little benefit and may reduce performance in some areas [4]. This implies that choosing the information to encode and the type of sonification to employ are important steps when seeking to produce a successful application [4]. Within this paper one approach to the problem of data selection for sonification is described and the results presented. The objective of the work is to produce a new audio interface for short range air-to-air missiles. Features of this task are a small specialist user group and a constrained choice of sonification schemes. Structured interviews were used to produce repertory grids based on the sounds heard and information required in current and ideal cases. This was followed up with a broader survey of system users. The results showed that the views of designers and users are often fundamentally different and that care is required to achieve a satisfactory result.
Neuregulin 3 and its roles in schizophrenia risk and presentation

Neuregulins, a four‐member family of epidermal growth factor‐like signaling molecules, have been studied for over two decades. They were first implicated in schizophrenia in 2002 with the detection of linkage and association at the NRG1 locus followed after a few years by NRG3. However, the associations with disease have not been very consistently observed. In contrast, association of NGR3 variants with disease presentation, specifically the presence of delusions, has been more consistent. This appears to be mediated by quantitative changes in the alternative splicing of the gene, which has also been consistently observed. Additional diseases and phenotypes, psychiatric or not, have also been connected with NRG3. These results demonstrate two important aspects of behavioral genetics research. The first is that if we only consider simple risk and fail to examine the details of each patient's individual phenotype, we will miss important insights on the disease biology. This is an important aspect of the goals of precision medicine. The second is that the functional consequences of variants are often more complex than simple alterations in levels of transcription of a particular gene, including, among others, regulation of alternative splicing. To accurately model and understand the biological consequences of phenotype—associated genetic variants, we need to study the biological consequences of each specific variant. Simply studying the consequences of a null allele of the orthologous gene in a model system, runs the risk of missing the many nuances of hypomorphic and/or gain of function variants in the genome of interest.