Miracle-dz/UniFAR-FTUs huggingface dataset:
A dielectric response study of the electronic stopping power of liquid water for energetic protons and a new I-value for water

The electronic stopping power of liquid water for protons over the 50 keV to 10 MeV energy range is studied using an improved dielectric response model which is in good agreement with the best available experimental data. The mean excitation energy (I) of stopping power theory is calculated to be 77.8 eV. Shell corrections are accounted for in a self-consistent manner through analytic dispersion relations for the momentum dependence of the dielectric function. It is shown that widely used dispersion schemes based on the random-phase approximation (RPA) can result in sizeable errors due to the neglect of damping and local field effects that lead to a momentum broadening and shifting of the energy-loss function. Low-energy Born corrections for the Barkas, Bloch and charge-state effects practically cancel out down to 100 keV proton energies. Differences with ICRU Report 49 stopping power values and earlier calculations are found to be at the ∼20% level in the region of the stopping maximum. The present work overcomes the limitations of the Bethe formula below 1 MeV and improves the accuracy of previous calculations through a more consistent account of the dielectric response properties of liquid water.
The Vascular Basement Membrane as “Soil” in Brain Metastasis

Brain-specific homing and direct interactions with the neural substance are prominent hypotheses for brain metastasis formation and a modern manifestation of Paget's “seed and soil” concept. However, there is little direct evidence for this “neurotropic” growth in vivo. In contrast, many experimental studies have anecdotally noted the propensity of metastatic cells to grow along the exterior of pre-existing vessels of the CNS, a process termed vascular cooption. These observations suggest the “soil” for malignant cells in the CNS may well be vascular, rather than neuronal. We used in vivo experimental models of brain metastasis and analysis of human clinical specimens to test this hypothesis. Indeed, over 95% of early micrometastases examined demonstrated vascular cooption with little evidence for isolated neurotropic growth. This vessel interaction was adhesive in nature implicating the vascular basement membrane (VBM) as the active substrate for tumor cell growth in the brain. Accordingly, VBM promoted adhesion and invasion of malignant cells and was sufficient for tumor growth prior to any evidence of angiogenesis. Blockade or loss of the β1 integrin subunit in tumor cells prevented adhesion to VBM and attenuated metastasis establishment and growth in vivo. Our data establishes a new understanding of CNS metastasis formation and identifies the neurovasculature as the critical partner for such growth. Further, we have elucidated the mechanism of vascular cooption for the first time. These findings may help inform the design of effective molecular therapies for patients with fatal CNS malignancies.
DRAMsim: a memory system simulator

As memory accesses become slower with respect to the processor and consume more power with increasing memory size, the focus of memory performance and power consumption has become increasingly important. With the trend to develop multi-threaded, multi-core processors, the demands on the memory system will continue to scale. However, determining the optimal memory system configuration is non-trivial. The memory system performance is sensitive to a large number of parameters. Each of these parameters take on a number of values and interact in fashions that make overall trends difficult to discern. A comparison of the memory system architectures becomes even harder when we add the dimensions of power consumption and manufacturing cost. Unfortunately, there is a lack of tools in the public-domain that support such studies. Therefore, we introduce DRAMsim, a detailed and highly-configurable C-based memory system simulator to fill this gap. DRAMsim implements detailed timing models for a variety of existing memories, including SDRAM, DDR, DDR2, DRDRAM and FB-DIMM, with the capability to easily vary their parameters. It also models the power consumption of SDRAM and its derivatives. It can be used as a standalone simulator or as part of a more comprehensive system-level model. We have successfully integrated DRAMsim into a variety of simulators including MASE [15], Sim-alpha [14], BOCHS[2] and GEMS[13]. The simulator can be downloaded from www.ece. umd.edu/dramsim.
Arabidopsis ATRX Modulates H3.3 Occupancy and Fine-Tunes Gene Expression

The Alpha Thalassemia-mental Retardation X-linked homolog functions as a H3.3 chaperone and modulates gene expression in Arabidopsis. Histones are essential components of the nucleosome, the major chromatin subunit that structures linear DNA molecules and regulates access of other proteins to DNA. Specific histone chaperone complexes control the correct deposition of canonical histones and their variants to modulate nucleosome structure and stability. In this study, we characterize the Arabidopsis thaliana Alpha Thalassemia-mental Retardation X-linked (ATRX) ortholog and show that ATRX is involved in histone H3 deposition. Arabidopsis ATRX mutant alleles are viable, but show developmental defects and reduced fertility. Their combination with mutants of the histone H3.3 chaperone HIRA (Histone Regulator A) results in impaired plant survival, suggesting that HIRA and ATRX function in complementary histone deposition pathways. Indeed, ATRX loss of function alters cellular histone H3.3 pools and in consequence modulates the H3.1/H3.3 balance in the cell. H3.3 levels are affected especially at genes characterized by elevated H3.3 occupancy, including the 45S ribosomal DNA (45S rDNA) loci, where loss of ATRX results in altered expression of specific 45S rDNA sequence variants. At the genome-wide scale, our data indicate that ATRX modifies gene expression concomitantly to H3.3 deposition at a set of genes characterized both by elevated H3.3 occupancy and high expression. Together, our results show that ATRX is involved in H3.3 deposition and emphasize the role of histone chaperones in adjusting genome expression.
Cross-sectional Microscopy Detection Technology for Subsurface Damage of Fixed Abrasive Lapped SiC Wafers

The sample preparation,corrosion fluid formula and corrosion environment of the cross-sectional microscopy detection for SiC wafer are systematically studied in this paper.The subsurface damage depth(SSD) and crack configurations of the(0001) Si surface and(0001) C surface of SiC wafer induced by fixed abrasive lapping are also analyzed.The results show that the damage observation is clear when the corrosion fluid formula ratio is KOH∶ K2CO3= 20 g∶ 1 g,the corrosion temperature is 420 ℃ and the corrosion time lasted for 3 minute.The SSD of fixed abrasive lapped SiC wafers is 2.6 μm when the lapping pressure is 2 psi with the diamond abrasive grit size of 14 μm. The micro-cracks configurations are vertical,oblique line,hooked,fork,dendritic,herringbone and horizontal line.The SSD of the(0001) Si surface and(0001) C surface of SiC wafer are basically consistent under the same processing conditions.
Automated breast tissue density assessment using high order regional texture descriptors in mammography

Breast cancer is the most common cancer and second leading cause of cancer death among women in the US. The relative survival rate is lower among women with a more advanced stage at diagnosis. Early detection through screening is vital. Mammography is the most widely used and only proven screening method for reliably and effectively detecting abnormal breast tissues. In particular, mammographic density is one of the strongest breast cancer risk factors, after age and gender, and can be used to assess the future risk of disease before individuals become symptomatic. A reliable method for automatic density assessment would be beneficial and could assist radiologists in the evaluation of mammograms. To address this problem, we propose a density classification method which uses statistical features from different parts of the breast. Our method is composed of three parts: breast region identification, feature extraction and building ensemble classifiers for density assessment. It explores the potential of the features extracted from second and higher order statistical information for mammographic density classification. We further investigate the registration of bilateral pairs and time-series of mammograms. The experimental results on 322 mammograms demonstrate that (1) a classifier using features from dense regions has higher discriminative power than a classifier using only features from the whole breast region; (2) these high-order features can be effectively combined to boost the classification accuracy; (3) a classifier using these statistical features from dense regions achieves 75% accuracy, which is a significant improvement from 70% accuracy obtained by the existing approaches.
Fabrication of Microchanneled Composites by Novel Selective Polymer Degradation

In this research a new low-cost, highly compatible method is proposed and demonstrated to create microchannels within carbon fiber reinforced polymeric (CFRP) composite laminates that caused a lower mechanical loss due to their presence. In it, microchannels were created within the CFRP composite laminate by selective degradation of the specially selected polymer, whose solid preforms were placed at specific locations within dry fabric layers during composite manufacturing by resin infusion. Interlaminar shear (ILSS) and three-point-bend flexural tests were carried out on CFRP composite laminates with and without microchannels of different diameters to assess their effect on structural strength. The results showed that inclusion of microchannels within the CFRP composite laminates decreased their ILSS and flexural strength, which decreased steadily with the increase in channel diameter. The mechanism for these observed results was found to be the creation of resin-rich areas, microchannels and lessened fiber content by the addition of microchannels. These mechanical testing results were compared with the results of CFRP composite laminates with microchannels, inserted by hollow glass tubes (HGTs), and it was found that the new applied strategy was quite effective in introducing microchannels within CFRP composite laminates with reduced mechanical loss and provided more space for additional functionalities.
Comparison of microscopic and endoscopic view of the internal acoustic meatus: A cadaveric study

The endoscope is thought to provide an improved exposure of the internal acoustic meatus after retrosigmoid craniotomy for microsurgical resection of intrameatal tumors. The aim of this study is to quantify the differences in internal acoustic meatus (IAM) exposure comparing microscopic and endoscopic visualization. A retrosigmoid approach was performed on 5 cadaver heads. A millimeter gauge was introduced into the internal acoustic meatus, and examinations with a surgical microscope and 0°, 30° and 70° rigid endoscopes were performed. The extent of IAM depth visualized with the microscope and the different angled endoscopes were analyzed. The microscopic view allowed an average IAM depth visualization of 2.8 mm. The endoscope allowed an improved exposure of IAM in all cases. The 0°, 30° and 70° endoscopes permitted an exposure that was respectively 96% (5.5 mm), 139% (6.7 mm) and 200% (8.4 mm) more lateral than the microscopic view. Angled optics, however, provided an image distortion, specifically the 70° endoscope. The endoscope provides a superior visualization of the IAM compared to the microscope when using a retrosigmoid approach. The 30° endoscope represented an ideal compromise of superior visualization with marginal image distortion. Additional implementation of the endoscope into microsurgery of intrameatal tumors likely facilitates complete tumor removal and might spare facial and vestibulocochlear function. Clin. Anat. 31:398–403, 2018. © 2017 Wiley Periodicals, Inc.
Age-Related Physical Changes Interfere With Judgments of Male Sexual Orientation From Faces

Although studies have shown that sexual orientation can be judged from faces, this research has not considered how age-related differences in perceivers or targets affect such judgments. In the current work, we evaluated whether accuracy differed among young adults (YA) and older adults (OA) for young and old men’s faces by recruiting a sample of YA and OA in the lab, a community sample of sexual minority men, and a sample of online participants. We found that OA and YA judged sexual orientation with similar accuracy. Perceptions of gender atypicality mediated the difference in judging older and younger targets’ sexual orientation. Although participants used positive affect to correctly discern sexual orientation regardless of target age, perceptions of masculinity were valid only for judgments of YA.
A Histone Map of Human Chromosome 20q13.12

Background We present a systematic search for regulatory elements in a 3.5 Mb region on human chromosome 20q13.12, a region associated with a number of medical conditions such as type II diabetes and obesity. Methodology/Principal Findings We profiled six histone modifications alongside RNA polymerase II (PolII) and CTCF in two cell lines, HeLa S3 and NTERA-2 clone D1 (NT2/D1), by chromatin immunoprecipitation using an in-house spotted DNA array, constructed with 1.8 kb overlapping plasmid clones. In both cells, more than 90% of transcription start sites (TSSs) of expressed genes showed enrichments with PolII, di-methylated lysine 4 of histone H3 (H3K4me2), tri-methylated lysine 4 of histone H3 (H3K4me3) or acetylated H3 (H3Ac), whereas mono-methylated lysine 4 of histone H3 (H3K4me1) signals did not correlate with expression. No TSSs were enriched with tri-methylated lysine 27 of histone H3 (H3K27me3) in HeLa S3, while eight TSSs (4 expressed) showed enrichments in NT2/D1. We have also located several CTCF binding sites that are potential insulator elements. Conclusions/Significance In summary, we annotated a number of putative regulatory elements in 20q13.12 and went on to verify experimentally a subset of them using dual luciferase reporter assays. Correlating this data to sequence variation can aid identification of disease causing variants.
Acute stimulation of a smooth muscle constrictor by oestradiol‐17&bgr; via GPER1 in bovine oviducts

Oviducts play roles in reproductive processes, including gametes transport, fertilization and early embryo development. Oviductal transport is controlled by various factors such as endothelins (EDNs) and nitric oxide (NO), smooth muscle contracting and relaxing factor, respectively. EDNs and NO production depend on an ovarian steroid hormone, oestradiol-17β (E2) and E2 quickly exerts their biological functions through G protein-coupled oestrogen receptor 1 (GPER1), which mediates rapid intracellular signalling. Because follicular fluid which contains a high concentration of E2 enters the oviduct, we hypothesized that E2 in the follicular fluid participates via GPER1 in producing EDNs and NO. To test this hypothesis, we investigated 1) the expression and localization of GPER1 in bovine oviductal tissues and 2) rapid effects of E2 via GPER1 on EDN1, EDN2 and inducible NO synthase (iNOS) expression in cultured bovine oviductal isthmic epithelial cells. GPER1 was observed in the oviductal epithelium, stroma and smooth muscle, and its expression was highest in the isthmus. Short-term treatments (≤1 hr) of E2 increased EDN2 mRNA expression in the isthmic epithelial cells, although E2 did not affect EDN1 and iNOS mRNA expressions. Results of GPER1-selective agonist G-1 and GPER1-selective antagonist G-15 treatments revealed acute stimulation by E2, which is mediated via GPER1. The overall findings suggested that E2 in follicular fluid rapidly stimulates EDN2 expression via GPER1 in the isthmic epithelial cells. Follicular fluid may play a role in retention of the ovulated oocyte in the end of ampulla by contracting the isthmus for successful fertilization.
The complete mitochondrial genome of Sinilabeo rendahli (Cypriniformes: Cyprinidae)

Abstract The Sinilabeo rendahli (S. rendahli) belongs to the family Cyprinidae and the order Cypriniformes, which is an economic fish species in southern China. In this study, the complete mitochondrial genome of S. rendahli was determined (the GenBank accession number is KT336714). The mitochondrial genome sequence of S. rendahli was a circular molecule with 16 586 bp in length, and it contained 37 typical animal mitochondrial genes including 2 ribosomal RNA genes, 13 protein-coding genes, 22 transfer RNA genes and a control region (D-loop). Four nucleotide compositions and their relative proportions of the entire mitogenome were, 26.62% C, 15.29% G, 32.31% A and 25.78% T, with an A + T and G + C contents being 58.09 and 41.91%, respectively.
Structural changes in DNA-binding proteins on complexation

Abstract Characterization and prediction of the DNA-biding regions in proteins are essential for our understanding of how proteins recognize/bind DNA. We analyze the unbound (U) and the bound (B) forms of proteins from the protein–DNA docking benchmark that contains 66 binary protein–DNA complexes along with their unbound counterparts. Proteins binding DNA undergo greater structural changes on complexation (in particular, those in the enzyme category) than those involved in protein–protein interactions (PPI). While interface atoms involved in PPI exhibit an increase in their solvent-accessible surface area (ASA) in the bound form in the majority of the cases compared to the unbound interface, protein–DNA interactions indicate increase and decrease in equal measure. In 25% structures, the U form has missing residues which are located in the interface in the B form. The missing atoms contribute more toward the buried surface area compared to other interface atoms. Lys, Gly and Arg are prominent in disordered segments that get ordered in the interface on complexation. In going from U to B, there may be an increase in coil and helical content at the expense of turns and strands. Consideration of flexibility cannot distinguish the interface residues from the surface residues in the U form.
Photoacoustic imaging for in vivo quantification of placental oxygenation in mice

Accurate analysis of placental and fetal oxygenation is critical during pregnancy. Photoacoustic imaging (PAI) combines laser technology with ultrasound in real time. We tested the sensitivity and accuracy of PAI for analysis of placental and fetal oxygen saturation (sO2) in mice. The placental labyrinth (L) had a higher sO2 than the junctional zone plus decidua region (JZ+D) in C57Bl/6 mice. Changing maternal O2 from 100 to 20% in C57Bl/6 mice lowered sO2 in these regions. C57Bl/6 mice were treated with the NO synthase inhibitor L‐NG‐nitroarginine methyl ester (L‐NAME) from gestational day (GD) 11 to GD18 to induce hypertension. L‐NAME decreased sO2 in L and JZ+D at GD14 and GD18 in association with fetal growth restriction and higher blood pressure. Hypoxia‐inducible factor 1a immunostaining was higher in L‐NAME vs. control mice at GD14. Fetal sO2 levels were similar between l‐NAME and control mice at GD14 and GD18. In contrast to untreated C57Bl/6, L‐NAME decreased placental sO2 at GD14 and GD18 vs. GD10 or GD12. Placental sO2 was lower in fetal growth restriction in an angiotensin‐converting enzyme 2 knockout mouse model characterized by placental hypoxia. On phantom studies, patterns of sO2 measured directly correlated with those measured by PAI. In summary, PAI enables the detection of placental and fetal oxygenation during normal and pathologic pregnancies in mice. —Yamaleyeva, L. M. , Sun, Y. , Bledsoe, T. , Hoke, A. , Gurley, S. B. , Brosnihan, K. B. Photoacoustic imaging for in vivo quantification of placental oxygenation in mice. FASEB J. 31, 5520–5529 (2017). www.fasebj. org
Neural Mechanisms of Reading Facial Emotions in Young and Older Adults

The ability to read and appropriately respond to emotions in others is central for successful social interaction. Young and older adults are better at identifying positive than negative facial expressions and also expressions of young than older faces. Little, however, is known about the neural processes associated with reading different emotions, particularly in faces of different ages, in samples of young and older adults. During fMRI, young and older participants identified expressions in happy, neutral, and angry young and older faces. The results suggest a functional dissociation of ventromedial prefrontal cortex (vmPFC) and dorsomedial prefrontal cortex (dmPFC) in reading facial emotions that is largely comparable in young and older adults: Both age groups showed greater vmPFC activity to happy compared to angry or neutral faces, which was positively correlated with expression identification for happy compared to angry faces. In contrast, both age groups showed greater activity in dmPFC to neutral or angry than happy faces which was negatively correlated with expression identification for neutral compared to happy faces. A similar region of dmPFC showed greater activity for older than young faces, but no brain-behavior correlations. Greater vmPFC activity in the present study may reflect greater affective processing involved in reading happy compared to neutral or angry faces. Greater dmPFC activity may reflect more cognitive control involved in decoding and/or regulating negative emotions associated with neutral or angry than happy, and older than young, faces.