Miracle-dz/UniFAR-FTUs huggingface dataset:
Integrative models of vascular remodeling during tumor growth

Malignant solid tumors recruit the blood vessel network of the host tissue for nutrient supply, continuous growth, and gain of metastatic potential. Angiogenesis (the formation of new blood vessels), vessel cooption (the integration of existing blood vessels into the tumor vasculature), and vessel regression remodel the healthy vascular network into a tumor‐specific vasculature that is in many respects different from the hierarchically organized arterio‐venous blood vessel network of the host tissues. Integrative models based on detailed experimental data and physical laws implement in silico the complex interplay of molecular pathways, cell proliferation, migration, and death, tissue microenvironment, mechanical and hydrodynamic forces, and the fine structure of the host tissue vasculature. With the help of computer simulations high‐precision information about blood flow patterns, interstitial fluid flow, drug distribution, oxygen and nutrient distribution can be obtained and a plethora of therapeutic protocols can be tested before clinical trials. In this review, we give an overview over the current status of integrative models describing tumor growth, vascular remodeling, blood and interstitial fluid flow, drug delivery, and concomitant transformations of the microenvironment. WIREs Syst Biol Med 2015, 7:113–129. doi: 10.1002/wsbm.1295
DNA bending-induced phase transition of encapsidated genome in phage λ

The DNA structure in phage capsids is determined by DNA–DNA interactions and bending energy. The effects of repulsive interactions on DNA interaxial distance were previously investigated, but not the effect of DNA bending on its structure in viral capsids. By varying packaged DNA length and through addition of spermine ions, we transform the interaction energy from net repulsive to net attractive. This allowed us to isolate the effect of bending on the resulting DNA structure. We used single particle cryo-electron microscopy reconstruction analysis to determine the interstrand spacing of double-stranded DNA encapsidated in phage λ capsids. The data reveal that stress and packing defects, both resulting from DNA bending in the capsid, are able to induce a long-range phase transition in the encapsidated DNA genome from a hexagonal to a cholesteric packing structure. This structural observation suggests significant changes in genome fluidity as a result of a phase transition affecting the rates of viral DNA ejection and packaging.
5 Influence of Exercise and Training on Motor Unit Activation

Human MUs vary considerably in twitch force, contractile speed, axonal conduction velocity, fatigue resistance, recruitment thresholds, firing rates, and firing patterns. These functional properties, together with the corresponding morphological characteristics such as soma size, axon diameter, and muscle fiber size, are interrelated. The smallest (soma size, axon diameter, muscle fiber size) MUs have the smallest twitch force, the slowest contraction speed, the slowest conduction velocity, the greatest resistance to fatigue, the lowest recruitment thresholds, and the lowest minimum and maximum firing rates. The converse applies to the largest MUs. Between the extremes are MUs with intermediate characteristics. MUs are generally recruited in order of size in voluntary contraction of increasing force or effort. Thus, units are recruited in order of increasing twitch force and contractile speed and decreasing resistance to fatigue. In some muscles MU recruitment occurs throughout the range of contraction force, whereas in other muscles most if not all MUs are recruited by about 50% of maximum contraction force. The latter pattern is characteristic of small muscles that perform precise movements. The recruitment order of MUs according to size is based on the inverse relation between susceptibility to discharge and motoneuron size. Thus, for evenly distributed and increasing excitatory synaptic input to a pool of motoneurons, smaller motoneurons will begin to fire before larger motoneurons. This arrangement ensures, for example, that the small, fatigue-resistant MUs will be preferentially activated in prolonged, low-intensity exercise, to which these units are most suited. In brief, intense exercise, the associated greater excitatory input will also recruit the large MUs, taking advantage of their greater strength and contractile speed. A frequent question is whether rapid, ballistic or explosive contractions and movements are associated with selective or preferential recruitment of large, fast twitch MUs. There is evidence of synaptic input systems that preferentially excite large, fast twitch MUs and inhibit small twitch MUs; however, the majority of evidence from human experiments indicates that the recruitment order is not reversed in ballistic contractions. For technical reasons, most studies have used isometric contractions, but recently successful recordings of single MUs have been made during locomotion. Future research must develop a successful recording arrangement for the study of recruitment and discharge properties of single MUs in large proximal muscles during activities such as kicking, jumping, and throwing. (ABSTRACT TRUNCATED AT 400 WORDS)
Neuropeptide S Reinstates Cocaine-Seeking Behavior and Increases Locomotor Activity through Corticotropin-Releasing Factor Receptor 1 in Mice

Neuropeptide S (NPS) is a recently discovered neuropeptide that increases arousal and wakefulness while decreasing anxiety-like behavior. Here, we used a self-administration paradigm to demonstrate that intracerebroventricular infusion of NPS reinstates extinguished cocaine-seeking behavior in a dose-dependent manner in mice. The highest dose of NPS (0.45 nm) increased active lever pressing in the absence of cocaine to levels that were equivalent to those observed during self-administration. In addition, we examined the role of the corticotropin-releasing factor receptor 1 (CRF1) in this behavior as well as locomotor stimulation and anxiolysis. CRF1 knock-out mice did not respond to either the locomotor stimulant or cocaine reinstatement effects of NPS, but still responded to its anxiolytic effect. The CRF1 antagonist antalarmin also blocked the increase in active lever responding in the reinstatement model and the locomotor activating properties of NPS without affecting its anxiolytic actions. Our results suggest that NPS receptors may be an important target for drug abuse research and treatment and that CRF1 mediates the cocaine-seeking and locomotor stimulant effects of NPS, but not its effects on anxiety-like behavior.
Effects of a Vigorous Gait on Mechanical Work and Oxygen Uptake during Treadmill Walking

This study was conducted to compare mechanical work during vigorous walking (which utilizes greater arm swings and step lengths) with that during normal walking and to examine whether individual differences (delta: vigorous walking – normal walking) in mechanical work during vigorous walking affected oxygen uptake (VO2). Six adult men (M age = 28.5yr., SD = 3.9) performed normal and vigorous walking on a treadmill at 1.11, 1.53, and 1.94 m/sec. At all speeds, external work during vigorous walking was greater than that during normal walking, and the delta of total work was significantly correlated with that of VO2. Thus, it was suggested that increased mechanical work (particularly total work) in vigorous walking would increase the metabolic cost.
Analysis of a few numerical integration methods for the Langevin equation

We study the position recurrence relation of several existing numerical integrators for the Langevin equation and use the modified equation approach to analyse their accuracy. We show that for the harmonic oscillator, the BBK integrator converges weakly with order 1 while the vGB82 and Langevin impulse (LÎ)‡ integrator converge weakly with order 2. We also study a restricted class of velocity definitions—those that lead to explicit starting procedures. We show that some recurrence relations exact for constant force, can achieve the exact virial relation by a proper definition of velocity, extending the result of Pastor et al. on the analysis of BBK integrators in 1988.
A systematic review of workplace disclosure and accommodation requests among youth and young adults with disabilities

Abstract Purpose: The objective of this systematic review is to critically appraise the literature on disability disclosure and workplace accommodations for youth and young adults with disabilities. Methods: Systematic searches of nine international databases identified 27 studies meeting our inclusion criteria. These studies were analyzed with respect to the characteristics of the participants, methodology, results of the studies and the quality of the evidence. Results: Among the 27 studies, 18,419 participants (aged 14–33, mean 23.9 years) were represented across seven countries. Barriers to disability disclosure and requests for workplace accommodations were found at the individual (i.e., disability type, severity, poor self-concept, and advocacy skills), employment (i.e., type of industry, and working conditions, lack of supports), and societal levels (i.e., stigma/discrimination). Facilitators of disability disclosure included individual factors (i.e., knowledge of supports and workplace rights, self-advocacy skills), employment (i.e., training/supports, effective communication with employers, realizing the benefits of accommodations), and societal factors (i.e., positive attitudes toward people with disabilities). There was little consensus on the processes and timing of how disability should be discussed in the workplace among youth with disabilities. Conclusions: Our findings highlight the complexities of disability disclosure for youth with disabilities. More studies are needed to explore issues of workplace disclosure and accommodations for young people to improve disclosure strategies and the process of providing appropriate accommodations. Implications for Rehabilitation Clinicians, educators, and parents should support youth to become self-aware and build self-advocacy skills so they can make an informed decision about how and when to disclose their condition to employers. Clinicians, educators, and employers should help youth with disabilities to understand the benefits of disclosing their disability, and educate them on the supports available so they can remain healthy and productive in the workplace. Clinicians should advocate for employers to create a positive and supportive environment where youth feel comfortable disclosing their condition.
A “Buffer” or “Boomerang?”— The Role of Corporate Reputation in Bad Times

Is a favorable prior reputation antibiotics or a hemlock cup in times of organizational crisis? To answer this question, the current study casts light on the contextual cues of crises by applying Brown and Dacin’s (1997) concepts of CA (corporate ability) and CSR (corporate social responsibility) and examines how the cues work in different crisis situations and affect the valence of reputation effects. Drawing on the expectancy violations (EV) theory and the cognitive dissonance perspectives, this study opens the door to reconciling contradicting research findings in literature and provides clues to why and when a good reputation yields buffering or boomerang effects in bad times.
Foreign Exchange and Oil Price Exposure in the Long Run: An Application to Oil Company Value page

This paper uses cointegration to evaluate long-run foreign exchange exposure. Since this technique requires exchange rates to be nonstationary, such that purchasing power parity does not hold in the long run, the analysis focuses on recent empirical findings suggesting that real exchange rates are nonstationary particularly because of oil price changes. Hence, the paper also estimates long-run oil price exposure, and investigates possible omitted variable bias from estimating foreign exchange exposure and oil price exposure separately. In order to focus the analysis, the paper explicitly considers an industry in which the combined effects of exchange rate and oil price changes are likely to be high: the global oil industry. Using the stock price as a metric of firm value, results of the cointegration analysis reveal that oil companies typically face statistically significant exchange rate and oil price exposures. The single-factor CAPM is thus inadequate as a long-run asset pricing model of oil companies, and a multi-factor model including exchange rates and oil prices in addition to the market portfolio is a superior long-run asset pricing model. Furthermore, models for the oil companies should include exchange rates and oil prices simultaneously in order to avoid omitted variable biases.
A mutation in the membrane subunit of an ABC transporter LolCDE complex causing outer membrane localization of lipoproteins against their inner membrane‐specific signals

Lipoproteins in Gram‐negative bacteria are anchored to the inner or outer membrane via fatty acids attached to the N‐terminal cysteine. The residue at position 2 determines the membrane specificity. An ATP binding cassette transporter LolCDE complex releases lipoproteins with residues other than aspartate at position 2 from the inner membrane, whereas those with aspartate at position 2 are rejected by LolCDE and therefore remain in the inner membrane. For further understanding of this rejection mechanism, a novel strategy was developed to select mutants in which lipoproteins with aspartate at position 2 are released. The isolated mutants carried an alanine to proline mutation at position 40 of LolC, a membrane subunit of the LolCDE complex. A significant portion of an inner membrane lipoprotein, L10P(DQ), was localized to the outer membrane when the LolC mutant was expressed. Periplasmic chaperone LolA formed a complex with the released L10P(DQ), which was subsequently incorporated into the outer membrane in a LolB‐dependent manner, indicating that neither LolA nor LolB rejects lipoproteins with aspartate at position 2. The amount of the LolC mutant co‐purified with LolD and LolE after membrane solubilization was reduced significantly. Taken together, these results indicate that the mutation causes destabilization of the LolCDE complex and concomitantly prevents the accurate recognition of lipoprotein‐sorting signals.
On the spectral efficiency of large CDMA systems using higher order modulation

The spectral efficiency of large CDMA systems using higher order modulation schemes is investigated. Therefore, the asymptotic analysis for single cell systems and random spreading codes is used to obtain the signal-to-interference-and-noise ratio (SINR) after the matched filter (MF) and linear minimum mean-squared-error (LMMSE) receiver. Then the concepts of capacity and cut-off rate are applied to determine the optimum spectral efficiency with coding and modulation. It is shown that with a MF receiver higher order modulation in combination with coding has no advantage. In contrast, beyond a particular signal-to-noise ratio (SNR) threshold the spectral efficiency of a CDMA system can be improved with larger constellations when deploying an LMMSE receiver. Depending on the SNR an optimum modulation scheme exists, which was shown for a number of QAM constellations.
Human parainfluenza virus types 1–4 in hospitalized children with acute lower respiratory infections in China

Human parainfluenza viruses (HPIVs) are an important cause of acute lower respiratory tract infections (ALRTIs). HPIV‐4, a newly identified virus, has been associated with severe ALRTIs recently. A total of 771 nasopharyngeal aspirate samples were collected from hospitalized children between March 2010 and February 2011. HPIVs were detected by Nest‐PCR, and other known respiratory viruses were detected by RT‐PCR and PCR. All amplification products were sequenced. HPIVs were detected in 151 (19.58%) patients, of whom 28 (3.63%) were positive for HPIV‐4, 12(1.55%) for HPIV‐1, 4 (0.51%) for HPIV‐2, and 107 (13.87%) for HPIV‐3. Only three were found to be co‐infected with different types of HPIVs. All HPIV‐positive children were under 5 years of age, with the majority being less than 1 year. Only the detection rate of HPIV‐3 had a significant statistical difference (χ2 = 29.648, P = 0.000) between ages. HPIV‐3 and HPIV‐4 were detected during the summer. Sixty (39.74%) were co‐infected with other respiratory viruses, and human rhinovirus (HRV) was the most common co‐infecting virus. The most frequent clinical diagnosis was bronchopneumonia, and all patients had cough; some patients who were infected with HPIV‐3 and HPIV‐4 had polypnea and cyanosis. No significant difference was found in clinical manifestations between those who were infected with HPIV‐4 and HPIV‐3. Two genotypes for HPIV‐4 were prevalent, although HPIV‐4a dominated. HPIV‐4 is an important virus for children hospitalized with ALRTIs in China. HRV was the most common co‐infecting virus. Two genotypes for HPIV‐4 are prevalent, HPIV‐4a dominated. J. Med. Virol. 88:2085–2091, 2016. © 2016 Wiley Periodicals, Inc.
Computational Modeling and Simulation of Thermal-Fluid Flow and Topology Formation in Laser Metal Additive Manufacturing

COMPUTATIONAL MODELING AND SIMULATION OF THERMAL-FLUID FLOW AND TOPOLOGY FORMATION IN LASER METAL ADDITIVE MANUFACTURING Name: Vincent, Timothy John University of Dayton Advisor: Dr. Markus P. Rumpfkeil The field of metal additive manufacturing holds great promise in several industries for its potential to reduce cost and open the doors to new design paradigms as well as agile and efficient logistical systems. However, the complex, multi-faceted physics of additive metals processing has proved to be a significant barrier to quickly deploying and utilizing this technology. The connection between processing parameters and build quality remains an active field of research, further complicated by the particular intricacies of each process implemented by various equipment manufacturers. As direct experimentation remains relatively costly in this field, a clear opportunity exists for developing accurate and cost efficient simulation tools to aid in untangling the relationships between process specifics and build outcomes. In this work, the salient physical phenomena were analyzed for a blown powder and a powder bed process. Models were then formulated based on this analysis to capture the effects of build parameters on micro-scale topology and temperature distributions. These models were then implemented using the OpenFOAM R ©Finite Volume software library. A steady-state model and simulation code was developed for the blown powder process and the topology predictions were validated quantitatively using experimental data from the literature. iii A time-dependent model and simulation code was developed for the powder bed process with an emphasis on capturing the complex interaction of thermally induced fluid flow with deformation of the gas-liquid interface of the melt pool. The salient aspects of this code were verified using simplified application cases and the code was demonstrated using a representative test case, which showed qualitative agreement with previous work. These two new codes enhance the field of additive metals processing by potentially reducing the effort necessary to produce parts by minimizing defects and maximizing microstructure quality.
Meta-Reasoning Algorithm for Improving Analysis of Student Interactions with Learning Objects using Supervised Learning

Supervised learning (SL) systems have been used to automatically learn models for analysis of learning object (LO) data. However, SL systems have trouble accommodating data from multiple distributions and “troublesome” data that contains irrelevant features or noise—all of which are relatively common in highly diverse LO data. The solution is to break up the available data into separate areas and then take steps to improve models on areas containing troublesome data. Unfortunately, finding these areas in the first place is a far from trivial task that balances finding a single distribution with having sufficient data to support meaningful analysis. Therefore, we propose a BoU metareasoning (MR) algorithm that first uses semi-supervised clustering to find compact clusters with multiple labels that each support meaningful analyses. After clustering, our BoU MR algorithm learns a separate model on each such cluster. Finally, our BoU MR algorithm uses feature selection (FS) and noise correction (NC) algorithms to improve models on clusters containing troublesome data. Our experiments, using three datasets containing over 5000 sessions of student interactions with LOs, show that multiple models from BoU MR achieve more accurate analyses than a single model. Further, FS and NC algorithms are more effective at improving multiple models than a single model.
Inhibition of G1 to S Phase Progression by a Novel Zinc Finger Protein P58TFL at P-bodies

We recently reported the translocation of the immunoglobulin (Ig) light chain κ locus gene with a possible tumor suppressor gene, TFL, in transformed follicular lymphoma. However, the functional significance in cell transformation remains to be elucidated. Here, we first identified two gene products, P58TFL and P36TFL, derived by alternative splicing. The expression was prominent in normal human lymphocytes but defective in some leukemia/lymphoma cell lines. Overexpression of either protein in a mouse pro-B cell line, Ba/F3, and a human leukemia cell line, Jurkat, inhibited G1 to S phase progression through suppression of retinoblastoma protein (Rb) phosphorylation. The dominant gene product, P58TFL, colocalized with mRNA-processing body markers, eukaryotic translation initiation factor 2C and DCP1 decapping-enzyme homolog A, but not with a stress granule maker, T-cell intracellular antigen 1, in the cytoplasm. Taken together with the unique CCCH-type zinc finger motif, the present study suggests that P58TFL could play an important role in the regulation of cell growth through posttranscriptional modification of cell cycle regulators, at least partially, upstream of Rb. (Mol Cancer Res 2009;7(6):880–9)
Interference Aware Cache Designs for Operating System Execution

Large-scale chip multiprocessors will likely be heterogeneous. It has been suggested by several groups that it may be worthwhile to implement some cores that are specially tuned to execute common code patterns. One such common application that will execute on all future processors is of course the operating system. Many future workloads will spend a large fraction of their execution time within privileged mode, either executing system calls or pure operating system functionality. Vast transistor budgets and relatively low on-chip communication latencies make it feasible to off-load the execution of privileged instruction sequences on to such a custom core. In this paper, we first examine this off-load approach and attempt to understand its benefits. We then try to architect a solution that captures the benefits of off-loading and eliminates its disadvantages. In essence, the benefits of offloading can be attributed to reduced cache interference, while its disadvantages are the high latency costs for off-load and cache coherence. Our proposed solution employs a special OS cache per core and improves performance by up to 18% for OS-intensive workloads without any significant addition of transistors. We consider several design choices for this OS cache and argue that it is a better use of transistor and power budget than the off-loading approach when both adding to the transistor budget or leaving it unchanged.