Miracle-dz/UniFAR-FTUs huggingface dataset:
Partial hessian fitting for determining force constant parameters in molecular mechanics

We present a new protocol for deriving force constant parameters that are used in molecular mechanics (MM) force fields to describe the bond‐stretching, angle‐bending, and dihedral terms. A 3 × 3 partial matrix is chosen from the MM Hessian matrix in Cartesian coordinates according to a simple rule and made as close as possible to the corresponding partial Hessian matrix computed using quantum mechanics (QM). This partial Hessian fitting (PHF) is done analytically and thus rapidly in a least‐squares sense, yielding force constant parameters as the output. We herein apply this approach to derive force constant parameters for the AMBER‐type energy expression. Test calculations on several different molecules show good performance of the PHF parameter sets in terms of how well they can reproduce QM‐calculated frequencies. When soft bonds are involved in the target molecule as in the case of secondary building units of metal‐organic frameworks, the MM‐optimized geometry sometimes deviates significantly from the QM‐optimized one. We show that this problem is rectified effectively by use of a simple procedure called Katachi that modifies the equilibrium bond distances and angles in bond‐stretching and angle‐bending terms. © 2016 Wiley Periodicals, Inc.
Nuclear structures in Tribolium castaneum oocytes

The first ultrastructural and immunomorphological characteristics of the karyosphere (karyosome) and extrachromosomal nuclear bodies in the red flour beetle, Tribolium castaneum, are presented. The karyosphere forms early in the diplotene stage of meiotic prophase by the gathering of all oocyte chromosomes in a limited nuclear volume. Using the BrUTP assay, T. castaneum oocyte chromosomes united in the karyosphere maintain their transcriptional activity until the end of oocyte growth. Hyperphosphorylated RNA polymerase II and basal transcription factors (TFIID and TFIIH) were detected in the perichromatin region of the karyosphere. The T. castaneum karyosphere has an extrachromosomal capsule that separates chromosomes from the rest of the nucleoplasm. Certain structural proteins (F‐actin, lamin B) were found in the capsule. Unexpectedly, the karyosphere capsule in T. castaneum oocytes was found to be enriched in TMG‐capped snRNAs, which suggests that the capsule is not only a structural support for the karyosphere, but may be involved in biogenesis of snRNPs. We also identified the counterparts of ‘universal’ extrachromosomal nuclear domains, Cajal bodies (CBs) and interchromatin granule clusters (IGCs). Nuclear bodies containing IGC marker protein SC35 display some features unusual for typical IGCs. SC35 domains in T. castaneum oocytes are predominantly fibrillar complex bodies that do not contain trimethyl guanosine (TMG)‐capped small nuclear (sn) RNAs. Microinjections of 2′‐O‐methyl (U)22 probes into the oocytes allowed revealing poly(A)+ RNAs in these nuclear domains. Several proteins related to mRNA export (heterogeneous ribonucleoprotein core protein A1, export adapters Y14 and Aly and export receptor NXF1) were also detected there. We believe that unusual SC35 nuclear domains of T. castaneum oocytes are possibly involved in mRNP but not snRNP biogenesis.
Cultural Effects on Cancer Prevention Behaviors: Fatalistic Cancer Beliefs and Risk Optimism Among Asians in Singapore

ABSTRACT Although culture is acknowledged as an important factor that influences health, little is known about cultural differences pertaining to cancer-related beliefs and prevention behaviors. This study examines two culturally influenced beliefs—fatalistic beliefs about cancer prevention, and optimistic beliefs about cancer risk—to identify reasons for cultural disparity in the engagement of cancer prevention behaviors. We utilized data from national surveys of European Americans in the United States (Health Information National Trends Survey 4, Cycle3; N = 1,139) and Asians in Singapore (N = 1,200) to make cultural comparisons. The odds of an Asian adhering to prevention recommendations were less than half the odds of a European American, with the exception of smoking avoidance. Compared to European Americans, Asians were more optimistic about their cancer risk both in an absolute and a comparative sense, and held stronger fatalistic beliefs about cancer prevention. Mediation analyses revealed that fatalistic beliefs and absolute risk optimism among Asians partially explain their lower engagement in prevention behaviors, whereas comparative risk optimism increases their likelihood of adhering to prevention behaviors. Our findings underscore the need for developing culturally targeted interventions in communicating cancer causes and prevention.
A Cross-Designed V-Blast Code Robust to Channel Correlation

The vertical Bell laboratory layered space-time (V-BLAST) code transmits independent data streams from each transmit antenna, and it may perform poorly over spatially correlated channels. To overcome this drawback, we present in this paper a cross-designed V-BLAST code, each component of which is, like a linear dispersion code, a combination of several transmitted symbols. Since the new code incorporates the advantages of V-BLAST and linear dispersion codes, it achieves robust performance to spatial correlation with low complexity, full transmission rate, and short decoding delay. Computer simulations demonstrate the efficiency of the proposed code by comparison with the V-BLAST and two typical full-diversity full-rate codes.
The Perception of Musical Rhythms

There are many musical sequences in which the rhythm is evident from the mere durations of the notes. A simple theory is proposed of how a listener may infer the rhythm of such a sequence by comparing the note lengths. It is assumed that the listener forms an idea of the rhythm as the sequence unfolds, constructing and eliminating metrical hypotheses in the light of what he hears. The theory, which differs in some important respects from earlier proposals, has been implemented as a computer program. The program has been tested on a wide variety of musical examples, and its successes and failures are discussed in detail.
Occupational exposure assessment in carbon nanotube and nanofiber primary and secondary manufacturers.

UNLABELLED RESEARCH SIGNIFICANCE: Toxicological evidence suggests the potential for a wide range of health effects, which could result from exposure to carbon nanotubes (CNTs) and carbon nanofibers (CNFs). The National Institute for Occupational Safety and Health (NIOSH) has proposed a recommended exposure limit (REL) for CNTs/CNFs at the respirable size fraction. The current literature is lacking exposure information, with few studies reporting results for personal breathing zone (PBZ) samples in occupational settings. To address this gap, exposure assessments were conducted at six representative sites identified as CNT/CNF primary or secondary manufacturers. METHODS Personal and area filter-based samples were collected for both the inhalable mass concentration and the respirable mass concentration of elemental carbon (EC) as well as CNT structure count analysis by transmission electron microscopy to assess exposures. When possible, full-shift PBZ samples were collected; area samples were collected on a task-based approach. RESULTS The vast majority of samples collected in this study were below the proposed REL (7 μg m(-3)). Two of the three secondary manufacturers' surveyed found concentrations above the proposed REL. None of the samples collected at primary manufacturers were found to be above the REL. Visual and microscopy-based evidence of CNTs/CNFs were found at all sites, with the highest CNT/CNF structure counts being found in samples collected at secondary manufacturing sites. The statistical correlations between the filter-based samples for the mass concentration of EC and CNT structure counts were examined. A general trend was found with a P-value of 0.01 and a corresponding Pearson correlation coefficient of 0.44. CONCLUSIONS CNT/CNF concentrations were above the proposed NIOSH REL for PBZ samples in two secondary manufacturing facilities that use these materials for commercial applications. These samples were collected during dry powder handling processes, such as mixing and weighing, using fairly large quantities of CNTs/CNFs.
Social Cognition, the Male Brain and the Autism Spectrum

Behavioral studies have shown that, at a population level, women perform better on tests of social cognition and empathy than men. Furthermore Autism Spectrum Disorders (ASDs), which are characterized by impairments in social functioning and empathy, occur more commonly in males than females. These findings have led to the hypothesis that differences in the functioning of the social brain between males and females contribute to the greater vulnerability of males to ASD and the suggestion that ASD may represent an extreme form of the male brain. Here we sought to investigate this hypothesis by determining: (i) whether males and females differ in social brain function, and (ii) whether any sex differences in social brain function are exaggerated in individuals with ASD. Using fMRI we show that males and females differ markedly in social brain function when making social decisions from faces (compared to simple sex judgements) especially when making decisions of an affective nature, with the greatest sex differences in social brain activation being in the inferior frontal cortex (IFC). We also demonstrate that this difference is exaggerated in individuals with ASD, who show an extreme male pattern of IFC function. These results show that males and females differ significantly in social brain function and support the view that sex differences in the social brain contribute to the greater vulnerability of males to ASDs.
Development of a discharge ontology to support postanesthesia discharge decision making

Postanesthesia discharge decision making is a challenging process due to the high complexity and variability of care provided to postoperative patients. We built an ontology-based decision support system that generates discharge recommendations for patients who have undergone surgical procedures. Discharge decisions are made based on patient vitals, symptoms, medical history and details of the surgical procedure. The output recommendations of our system can aid healthcare providers in discharge decision-making and potentially reduce readmissions due to improper discharge. This project demonstrates the potential uses of ontologies in medical decision support systems, especially in areas that use specific scoring guidelines to aid decision-making.
Shear strength of reinforced concrete beams with recycled aggregates

This article presents an experimental program on the shear behavior of beams without transversal reinforcement manufactured with natural aggregate concrete and 100% recycled aggregate concrete. The beams were tested under four-point bending for a shear span-to-depth ratio (a/d) equal to 1.5 and 3.0. The mechanical properties of two mixes were characterized in terms of compressive strength, splitting tensile strength, and elastic modulus. Three-point bending tests were performed on plain pre-notched samples in order to determine the fracture properties by an inverse analysis of experimental force–crack mouth opening displacement curves using the analytical nonlinear hinge model and a power law strain-softening relationship. The strain-softening law is described by two parameters being, respectively, the power n and the critical crack opening displacement wc. The experimental results show that, for the same class of compressive strength, tensile strength, fracture energy, and the shear strength of recycled aggregate concrete are lower than natural aggregate concrete. The decrease in the fracture energy and the shear strength is consistent with the decrease in the splitting tensile strength of the recycled aggregate concrete mixes compared to the natural aggregate concrete. Critical shear crack theory was adopted to model the shear behavior of beams tested with a/d = 3.0. For an accurate evaluation of the deformation capacity of tested beams, the nonlinear hinge model for recycled concrete members was extended to recycled concrete sections. For deep beams (a/d = 1.5), the strut-and-tie model was used. Finally, comparisons of prediction models to a wide range of experimental data are presented.
Epigenetic Signatures at the RUNX2‐P1 and Sp7 Gene Promoters Control Osteogenic Lineage Commitment of Umbilical Cord‐Derived Mesenchymal Stem Cells

Wharton's Jelly mesenchymal stem cells (WJ‐MSCs) are an attractive potential source of multipotent stem cells for bone tissue replacement therapies. However, the molecular mechanisms involved in their osteogenic conversion are poorly understood. Particularly, epigenetic control operating at the promoter regions of the two master regulators of the osteogenic program, RUNX2/P57 and SP7 has not yet been described in WJ‐MSCs. Via quantitative PCR profiling and chromatin immunoprecipitation (ChIP) studies, here we analyze the ability of WJ‐MSCs to engage osteoblast lineage. In undifferentiated WJ‐MSCs, RUNX2/P57 P1, and SP7 promoters are found deprived of significant levels of the histone post‐translational marks that are normally associated with transcriptionally active genes (H3ac, H3K27ac, and H3K4me3). Moreover, the RUNX2 P1 promoter lacks two relevant histone repressive marks (H3K9me3 and H3K27me3). Importantly, RUNX2 P1 promoter is found highly enriched in the H3K4me1 mark, which has been shown recently to mediate gene repression of key regulatory genes. Upon induction of WJ‐MSCs osteogenic differentiation, we found that RUNX2/P57, but not SP7 gene expression is strongly activated, in a process that is accompanied by enrichment of activating histone marks (H3K4me3, H3ac, and H3K27ac) at the P1 promoter region. Histone mark analysis showed that SP7 gene promoter is robustly enriched in epigenetic repressive marks that may explain its poor transcriptional response to osteoblast differentiating media. Together, these results point to critical regulatory steps during epigenetic control of WJ‐MSCs osteogenic lineage commitment that are relevant for future applications in regenerative medicine. J. Cell. Physiol. 232: 2519–2527, 2017. © 2016 Wiley Periodicals, Inc.
activates Nrf 2 / antioxidant response element signaling pathway in both neuronal and microglial cells : therapeutic relevance to neurodegenerative disease ☆

Oxidative stress and neuroinflammation are hallmarks of neurodegenerative diseases, which do not play independently but work synergistically through complex interactions exacerbating neurodegeneration. Therefore, the mechanism that is directly implicated in controlling oxidative stress and inflammatory response could be an attractive strategy to prevent the onset and/or delay the progression of neurodegenerative diseases. The transcription factor nuclear factorE2-related factor-2 (Nrf2) is the guardian of redox homeostasis by regulating a battery of antioxidant and phase II detoxification genes, which are relevant to defense mechanism against oxidative stress and inflammatory responses. In this study, we show that a recently identified Glycyrrhiza-inflata-derived chalcone, licochalcone E (Lico-E), attenuates lipopolysaccharide-induced inflammatory responses in microglial BV2 cells and protects dopaminergic SH-SY5Y cells from 6hydroxydopamine cytotoxicity. Lico-E activates Nrf2-antioxidant response element (ARE) system and up-regulates downstream NAD(P)H:quinone oxidoreductase 1 (NQO1) and heme oxygenase-1 (HO-1). Anti-inflammatory and cytoprotective effects of Lico-E are attenuated in siRNA-mediated Nrf2silencing cells as well as in the presence with specific inhibitor of HO-1 or NQO1, respectively. Lico-E also has neuroprotective effect against 1-methyl-4-phenyl1,2,3,6-tetrahydropyridine-induced nigrostriatal dopaminergic neurodegeneration in mice, with up-regulation of HO-1 and NQO1 in the substantia nigra of the brain. This study demonstrates that Lico-E is a potential activator of the Nrf2/ARE-dependent pathway and is therapeutically relevant not only to oxidativestress-related neurodegeneration but also inflammatory responses of microglial cells both in vitro and in vivo. © 2012 Elsevier Inc. All rights reserved.
Nuclear entry of DNA viruses

DNA viruses undertake their replication within the cell nucleus, and therefore they must first deliver their genome into the nucleus of their host cells. Thus, trafficking across the nuclear envelope is at the basis of DNA virus infections. Nuclear transport of molecules with diameters up to 39 nm is a tightly regulated process that occurs through the nuclear pore complex (NPC). Due to the enormous diversity of virus size and structure, each virus has developed its own strategy for entering the nucleus of their host cells, with no two strategies alike. For example, baculoviruses target their DNA-containing capsid to the NPC and subsequently enter the nucleus intact, while the hepatitis B virus capsid crosses the NPC but disassembles at the nuclear side of the NPC. For other viruses such as herpes simplex virus and adenovirus, although both dock at the NPC, they have each developed a distinct mechanism for the subsequent delivery of their genome into the nucleus. Remarkably, other DNA viruses, such as parvoviruses and human papillomaviruses, access the nucleus through an NPC-independent mechanism. This review discusses our current understanding of the mechanisms used by DNA viruses to deliver their genome into the nucleus, and further presents the experimental evidence for such mechanisms.
Terahertz imaging radar with aperture synthetic techniques for object detection

Terahertz imaging is considered as a promising detection and imaging method with wide application prospect in security inspection and counter-terrorism. In this paper, we present a frequency-modulated continuous-wave (FMCW) imaging radar with phase coherent reception. The proposed radar scheme works at 240GHz with a bandwidth of 4.8GHz. The basic functionality of the radar has been verified experimentally and the results demonstrate that the effective range resolution is better than 4cm, in the condition without the compensation of chirp nonlinearity of the transmitted wave. In addition, to verify the imaging performance of THz radar, an ISAR experiment is performed and the imaging result shows that the imaging radar can achieve high resolution in the range and azimuth dimension.
Haptics for Product Design and Manufacturing Simulation

Product design and manufacturing simulation is a promising research and application area for haptics. By benefiting from its natural human-computer interaction and realistic force/torque feedback, haptics can change the traditional design and manufacturing approaches which are mainly based on physical mock-ups or CAD (Computer Aided Design) modes. This paper provides a detailed and comprehensive survey of haptics for product design and manufacturing simulation in the past 10 years, mainly from 2004-2014, including haptics for product design and shape modelling, haptics for machining simulation, and haptics for virtual assembly and maintenance simulation. The new haptic devices and rendering algorithms involved in this area are introduced, the major research efforts and the typical systems are discussed, and the new ideas and research progresses are investigated. Then, conclusions and future trends are summarized.
FY 1993 progress report on the ANS thermal-hydraulic test loop operation and results

The Thermal-Hydraulic Test Loop (THTL) is an experimental facility constructed to support the development of the Advanced Neutron Source Reactor (ANSR) at Oak Ridge National Laboratory (ORNL). Highly subcooled heavy-water coolant flows vertically upward at a very high mass flux of almost 27 MG/m{sup 2}-s. In a parallel fuel plate configuration as in the ANSR, the flow is subject to a potential excursive static-flow instability that can very rapidly lead to flow starvation and departure from nucleate boiling (DNB) in the ``hot channel``. The current correlations and experimental data bases for flow excursion (FE) and critical heat flux (CHF) seldom evaluate the specific combination of ANSR operating parameters. The THTL facility was designed and built to provide known thermal-hydraulic (T/H) conditions for a simulated full-length coolant subchannel of the ANS reactor core, thus facilitating experimental determination of FE and CHF thermal limits under expected ANSR T/H conditions. A series of FE tests with water flowing vertically upward was completed over a nominal heat flux range of 6 to 17 MW/m{sup 2}, a mass flux range of 8 to 28 Mg/m{sup 2}-s, an exit pressure range of 1.4 to 2.1 MPa, and an inlet temperature range of 40 to 50 C. more » FE experiments were also conducted using as ``soft`` a system as possible to secure a true FE phenomena (actual secondary burnout). True DNB experiments under similar conditions were also conducted. To the author`s knowledge, no other FE data have been reported in the literature to date that dover such a combination of conditions of high mass flux, high heat flux, and moderately high pressure. « less
Competitive index in mixed infections: a sensitive and accurate assay for the genetic analysis of Pseudomonas syringae-plant interactions.

SUMMARY Mixed infections have been broadly applied to the study of bacterial pathogens in animals. However, the application of mixed infection-based methods in plant pathogens has been very limited. An important factor for this limitation is the different dynamics that mixed infections have been reported to show in the different types of models. Reports in systemic animal infections have shown that any bacterium has the same probability of multiplying within a mixed infection than in a single infection. However, in plant pathogens, bacterial growth in a mixed infection does not seem to reflect growth in a single infection, as growth interference takes place between the co-inoculated strains. Here we show that growth interference in mixed infection between different Pseudomonas syringae strains is not intrinsic to growth within a plant host, but dependent on the dose of inoculation. We also show that the minimal inoculation dose required to avoid interference depends on the aggressiveness of the pathogen as well as the type of virulence factor that differentiates the co-inoculated strains. This study establishes the basis for the use of mixed infection-based applications to the study of phytopathogenic bacteria. Analysis of the virulence of a type III effector mutant and an hrp regulatory mutant illustrate the increased accuracy and sensitivity of competitive index assays vs. regular growth assays. Several applications of this assay are addressed, and potential implications for this and other mixed infection-based methods are discussed.
Scalability for clustering algorithms revisited

ABSTRACT This paper presents a simple new algorithm that performs k-means clustering in one scan of a dataset, while using a bu er for points from the dataset of xed size. Experiments show that the new method is several times faster than standard k-means, and that it produces clusterings of equal or almost equal quality. The new method is a simpli cation of an algorithm due to Bradley, Fayyad and Reina that uses several data compression techniques in an attempt to improve speed and clustering quality. Unfortunately, the overhead of these techniques makes the original algorithm several times slower than standard k-means on materialized datasets, even though standard k-means scans a dataset multiple times. Also, lesion studies show that the compression techniques do not improve clustering quality. All results hold for 400 megabyte synthetic datasets and for a dataset created from the real-world data used in the 1998 KDD data mining contest. All algorithm implementations and experiments are designed so that results generalize to datasets of many gigabytes and larger.