Miracle-dz/UniFAR-FTUs huggingface dataset:
Implementation of Replica Exchange with Dynamic Scaling in GROMACS 2018

This Honors Thesis-Unrestricted is protected by copyright and/or related rights. It has been brought to you by ScholarWorks@UNO with permission from the rights-holder(s). You are free to use this Honors Thesis-Unrestricted in any way that is permitted by the copyright and related rights legislation that applies to your use. For other uses you need to obtain permission from the rights-holder(s) directly, unless additional rights are indicated by a Creative Commons license in the record and/or on the work itself.
An Inverted U Relationship between Competition and Innovation: A Revisit

This paper oﬀers three possible reasons for an inverted U relationship between competition and innovation. They are based on the ideas of multidirectional innovation, cumulative innovation and rent protection activity. These explanations complement the escape competition eﬀect identiﬁed by Aghion, Bloom, Blundell, Griﬃth, and Howitt (2005). deregulation, all of which tend to promote competition. (iii) Geroski (1995) shows that there exists a strong negative correlationship between innovation and market concentration and a strong positive correlationship between market entry and innovation. (iv) According to Gald´on-S´anchez and Schmitz (2001), the collapse of world steel production in the early 1980’s led to signiﬁcant productivity gains by iron-ore mines due to intensiﬁed competition. (v) Holmes and Schmitz (2001) argue that monopoly was pervasive in the U.S. water transportation in the 19th and 20th centuries, but subsequently prices fell and fewer ineﬃcient technologies were used due to competition of railroads. (vi) Nickell (1996) demonstrates that TFP growth has a strong correlation with the number of ﬁrms. (vii) Blundell, Griﬃth, and Van Reenen (1999) show that competition in the product market promotes innovation, controlling unobserved ﬁrm speciﬁc heterogeneity. Aghion and (1992) for discussion of the quality-ladder model of
microRNA-451 Regulates Macrophage Migration Inhibitory Factor Production and Proliferation of Gastrointestinal Cancer Cells

Purpose: microRNAs (miRNA) are small RNAs that function as post-transcriptional regulators of gene expression. Recent evidence has shown that some miRNAs can act as oncogenes or tumor suppressors. This study was conducted to evaluate the potential association of miRNA expression with clinical outcome in patients with gastric cancer. Experimental Design: Expression of 250 human mature miRNAs was measured by real-time PCR on paraffin-embedded tumor samples of 21 patients with gastric cancer stage III uniformly treated with surgical resection followed by chemoradiation. We identified the miRNAs correlated with disease-free and overall survival times, and the results were evaluated including 24 other patients. In vitro cell proliferation and radiosensitivity studies were done to support clinical data. Results: The results revealed that down-regulation of miR-451 was associated with worse prognosis. miR-451 was detected by in situ hybridization in epithelial cells and showed decreased expression in gastric and colorectal cancer versus nontumoral tissues. Overexpression of miR-451 in gastric and colorectal cancer cells reduced cell proliferation and increased sensitivity to radiotherapy. Microarray and bioinformatic analysis identified the novel oncogene macrophage migration inhibitory factor (MIF) as a potential target of miR-451. In fact, overexpression of miR-451 down-regulated mRNA and protein levels of MIF and decreased expression of reporter genes with MIF target sequences. Moreover, we found a significant inverse correlation between miR-451 and MIF expression in tumoral gastric biopsies. Conclusions: These findings support the role of miR-451 as a regulator of cancer proliferation and open new perspectives for the development of effective therapies for chemoradioresistant cancers.
Genome-wide mapping of TnrA-binding sites provides new insights into the TnrA regulon in Bacillus subtilis

Under nitrogen limitation conditions, Bacillus subtilis induces a sophisticated network of adaptation responses. More precisely, the B. subtilis TnrA regulator represses or activates directly or indirectly the expression of a hundred genes in response to nitrogen availability. The global TnrA regulon have already been identified among which some directly TnrA‐regulated genes have been characterized. However, a genome‐wide mapping of in vivo TnrA‐binding sites was still needed to clearly define the set of genes directly regulated by TnrA. Using chromatin immunoprecipitation coupled with hybridization to DNA tiling arrays (ChIP‐on‐chip), we now provide in vivo evidence that TnrA reproducibly binds to 42 regions on the chromosome. Further analysis with real‐time in vivo transcriptional profiling, combined with results from previous reports, allowed us to define the TnrA primary regulon. We identified 35 promoter regions fulfilling three criteria necessary to be part of this primary regulon: (i) TnrA binding in ChIP‐on‐chip experiments and/or in previous in vitro studies; (ii) the presence of a TnrA box; (iii) TnrA‐dependent expression regulation. In addition, the TnrA primary regulon delimitation allowed us to improve the TnrA box consensus. Finally, our results reveal new interconnections between the nitrogen regulatory network and other cellular processes.
Conditioned flavor aversions to familiar tap water in rats: an adjustment with implications for aversion therapy treatment of alcoholism and obesity.

Conditioned flavor aversions, readily established in rats by pairing a novel palatable flavor with radiation-induced or drug-induced illness, are highly efficient adjustments with implications for the treatment of alcoholism and obesity. Recent experiments show that such aversion acquisition is diminished by preconditioning familiarity with the conditioned stimulus (CS) flavor. However, these studies involved single pairings of the target flavor with postingestional illness. In the present experiment, multiple conditioning trials and discrimination training were combined to produce a marked aversion to a highly familiar and relatively bland substance, plain tap water. This conditioned water aversion demonstrates the transient nature of the CS familiarity effect, thus weakening any contention that preconditioning exposure to target flavors will necessarily render aversion therapy for alcoholism or obesity ineffective.
Target Space Duality in Noncommutative Geometry

The structure of spacetime duality and discrete world sheet symmetries of compactified string theory is examined within the framework of noncommutative geometry. The full noncommutative string spacetime is constructed using the Fr{umlt o}hlich-Gawedzki spectral triple which incorporates the vertex operator algebra of the string theory. The duality group appears naturally as a subgroup of the automorphism group of the vertex operator algebra and spacetime duality is shown to arise as the possibility of associating two independent Dirac operators, arising from the chiral structure of the world sheet theory, to the noncommutative geometry. {copyright} {ital 1997} {ital The American Physical Society}
Graphical symbol retrieval using a branch and bound algorithm

Graphical symbol spotting and retrieval in document images is an important sub-field in document analysis. This paper presents a branch and bound algorithm for spotting a queried graphical symbol in documents. The technique utilizes geometric primitives as feature points. The preprocessing of the input images involves applying some ordinary morphological operations and then sampling to get points or segments. As for the search; a branch and bound geometric matching algorithm is used to locate the required symbol(s) in the documents. The presented method has been tested on documents that contain electronic circuits and it achieved high accuracy.
SPLIT PHASE PROCESSING FOR ULTRASOUND SPECKLE REDUCTION: SIMULATED AND REAL DATA COMPARATIVE RESULTS

B-mode ultrasound images are characterised by the speckle artefact, which introduces fine-false structures whose apparent resolution is beyond the imaging system capabilities. Two widely used methods destined for speckle reduction are: a) split spectrum processing (SSP), and b) angular compounding. The first one is responsible for a significant resolution loss introduced in the final image. The second method requires a set of images scanned from different directions - a critical limitation in medical practice. Here, we propose a new speckle reduction technique that tackles the problem adjoining the characteristics of both angular compounding and SSP methods, but without their drawbacks. We have called it ‘Split Phase Processing’ (SPP) because it processes 2D data by using 2D directive filters to split the RF ultrasound image into a set of wide-band images with different phases. The outcomes of applying SPP to images generated by simulated and real laboratory acquired ultrasound pulses are shown.
Strong association between failure of T cell homeostasis and the syncytium-inducing phenotype among HIV-1-infected men in the Amsterdam Cohort Study

ObjectiveTo assess the association between T cell homeostasis and its failure and 1. ) the occurence of AIDS and 2. ) the switch from the non-syncytium-inducing (NSI) to the syncytium-inducing (SI) HIV virus phenotype. MethodsFor each of 325 homosexual men in the Amsterdam Cohort Study, the slope of the CD3 T cell count versus time was determined. The timing (T cell inflection point (IP)) and magnitude of the change in slope were correlated with the time of the NSI/SI switch. ResultsMedian T cell slopes before the IP (pre-IP) were nearly zero regardless of whether AIDS occurred; the slopes after the IP (post-IP) were associated with clinical outcomes, with a median annual decline of 17.6% among those who developed AIDS and increase of 4.6% in those remaining AIDS free. Among subjects considered to have a true IP (decline > 8.2%/year post-IP), the times of the SI switch and the IP slope were highly correlated (r = 0.65); among those with AIDS, the SI switch preceded the IP by a median of 0.63 years. ConclusionThese results support the concept of blind T cell homeostasis and also suggest that HIV-1 SI variants play an important role in the failure of T cell homeostasis.
Diversified Method in Teaching and Learning Muamalat towards Sustainable Legal Education in Islamic Finance

The Faculty of Law at Universiti Kebangsaan Malaysia (herein after referred to as UKM) has always aspired to produce law graduates who are able to serve both the civil as well as the shariah legal fraternities. The shariah legal industry was equally critical on these new law graduates as the quality of new shariah lawyers came under scrutiny. Such developments have further driven the Law Faculty of UKM to further improve the teaching and learning aspects of these shariah courses. This has of course triggered a revamp in the teaching and learning of the course of Muamalat at the Law Faculty. The aim of this paper is to explain the importance of diversified teaching method in Muamalat Courses. Survey method were adopted in analysing the effectiveness of the diversified method. The findings of the surveys showed that diversified method is relevant in teaching and learning Muamalat combining lectures, tutorials as well as Muamalat Interactive Game (MIG) in ensuring the understanding of the muamalat principles to the students.
Hybrid chaos-based image encryption approach using block and stream ciphers

Due to their fundamental features, chaotic maps are very suitable for various image encryption schemes. Most of the proposed discrete chaotic cryptographic approaches are based on stream or block cipher schemes. If these two schemes are combined the security level is improved by enhancing the encryption process complexity, the key space and the robustness of the cryptosystem. In the beginning, the image is divided into two sub-images. Next, these two sub-images are encrypted using respectively stream and block cipher schemes. After that, the two sub-images are merged to create enciphered image. Simulation results have shown the effectiveness and the robustness of the proposed scheme.
Balancing Proliferation with Igκ Recombination during B-lymphopoiesis

The essential events of B-cell development are the stochastic and sequential rearrangement of immunoglobulin heavy (Igμ) and then light chain (Igκ followed by Igλ) loci. The counterpoint to recombination is proliferation, which both maintains populations of pro-B cells undergoing Igμ recombination and expands the pool of pre-B cells expressing the Igμ protein available for subsequent Igκ recombination. Proliferation and recombination must be segregated into distinct and mutually exclusive developmental stages. Failure to do so risks aberrant gene translocation and leukemic transformation. Recent studies have demonstrated that proliferation and recombination are each affected by different and antagonistic receptors. The IL-7 receptor drives proliferation while the pre-B-cell antigen receptor, which contains Igμ and surrogate light chain, enhances Igκ accessibility and recombination. Remarkably, the principal downstream proliferative effectors of the IL-7R, STAT5 and cyclin D3, directly repress Igκ accessibility through very divergent yet complementary mechanisms. Conversely, the pre-B-cell receptor represses cyclin D3 leading to cell cycle exit and enhanced Igκ accessibility. These studies reveal how cell fate decisions can be directed and reinforced at each developmental transition by single receptors. Furthermore, they identify novel mechanisms of Igκ repression that have implications for gene regulation in general.
Nicotine Selectively Enhances NMDA Receptor-Mediated Synaptic Transmission during Postnatal Development in Sensory Neocortex

The neurotransmitters acetylcholine (ACh) and glutamate have been separately implicated in synaptic plasticity during development of sensory neocortex. Here we show that these neurotransmitters can, in fact, act synergistically via their actions at nicotinic ACh receptors (nAChRs) and NMDA receptors, respectively. To determine how activation of nAChRs modifies glutamatergic EPSPs, we made whole-cell recordings from visualized pyramidal neurons in slices of rat auditory cortex. Pulsed (pressure) ejection of nicotine onto apical dendrites selectively enhanced EPSPs mediated by NMDA receptors without affecting AMPA/kainate (AMPA/KA) receptor-mediated EPSPs. The enhancement occurred during a transient, postnatal period of heightened cholinergic function [neurons tested on postnatal day 8–16 (P8–16)], and not in the mature cortex (>P19). Three related findings indicated the mechanism of action: (1) The specific α7 nAChR antagonist methyllycaconitine citrate (MLA) blocked the effect of nicotine; (2) pulsed nicotine did not enhance postsynaptic depolarizations induced by iontophoretically applied NMDA; and (3) bath exposure to nicotine for several minutes produced apparent nAChR desensitization and precluded enhancement of EPSPs by pulsed nicotine. Together, the data suggest that nicotine acts at rapidly desensitizing, presynaptic α7 nAChRs to increase glutamate release onto postsynaptic NMDA receptors. The synergistic actions mediated by α7 nAChRs and NMDA receptors may contribute to experience-dependent synaptic plasticity in sensory neocortex during early postnatal life.
Early-onset, slow progression of cone photoreceptor dysfunction and degeneration in CNG channel subunit CNGB3 deficiency.

PURPOSE To investigate the progression of cone dysfunction and degeneration in CNG channel subunit CNGB3 deficiency. METHODS Retinal structure and function in CNGB3(-/-) and wild-type (WT) mice were evaluated by electroretinography (ERG), lectin cytochemistry, and correlative Western blot analysis of cone-specific proteins. Cone and rod terminal integrity was assessed by electron microscopy and synaptic protein immunohistochemical distribution. RESULTS Cone ERG amplitudes (photopic b-wave) in CNGB3(-/-) mice were reduced to approximately 50% of WT levels by postnatal day 15, decreasing further to approximately 30% of WT levels by 1 month and to approximately 20% by 12 months of age. Rod ERG responses (scotopic a-wave) were not affected in CNGB3(-/-) mice. Average CNGB3(-/-) cone densities were approximately 80% of WT levels at 1 month and declined slowly thereafter to only approximately 50% of WT levels by 12 months. Expression levels of M-opsin, cone transducin α-subunit, and cone arrestin in CNGB3(-/-) mice were reduced by 50% to 60% by 1 month and declined to 35% to 45% of WT levels by 9 months. In addition, cone opsin mislocalized to the outer nuclear layer and the outer plexiform layer in the CNGB3(-/-) retina. Cone and rod synaptic marker expression and terminal ultrastructure were normal in the CNGB3(-/-) retina. CONCLUSIONS These findings are consistent with an early-onset, slow progression of cone functional defects and cone loss in CNGB3(-/-) mice, with the cone signaling deficits arising from disrupted phototransduction and cone loss rather than from synaptic defects.
An Analytical Model and Performance Analysis of Shared Buffer ATM Switches under Non-uniform Traffic

For uniform traffic, ATM switches employing shared buffering have lower cell loss probability and better buffer utilization than other buffering strategies. However, the performance of shared-buffer switches degrades dramatically under non-uniform traffic. Traffic nonuniformity is inherent in telecommunications, and is likely to be present in ATM networks because of the different characteristics of traffic sources such as video, voice and data. A number of buffer management schemes which are designed to overcome the adverse effect of non-uniform traffic in shared-buffer ATM switches have been proposed and studied. In this paper, we analyse the pushout technique to purge hot-spot cells which unfairly occupy the buffer. We call it Hot-Spot Pushout (HSPO). We develop an analytical model for buffer sharing with and without HSPO under non-uniform traffic and validate it using simulation. We also simulate other buffer sharing schemes available in the literature and show that HSPO performs consistently better than all of them in the presence of non-uniform traffic.
An Improved Upper Complexity Bound for the Topology Computation of a Real Algebraic Plane Curve

The computation of the topological shape of a real algebraic plane curve is usually driven by the study of the behavior of the curve around its critical points (which includes also the singular points). In this paper we present a new algorithm computing the topological shape of a real algebraic plane curve whose complexity is better than the best algorithms known. This is due to the avoiding, through a sufficiently good change of coordinates, of real root computations on polynomials with coefficients in a simple real algebraic extension of Q to deal with the critical points of the considered curve. In fact, one of the main features of this algorithm is that its complexity is dominated by the characterization of the real roots of the discriminant of the polynomial defining the considered curve.
The Influence of Spiritual and Emotional Intelligence on Romantic Relationships of African Americans

The Influence of Spiritual and Emotional Intelligence on Romantic Relationships of African Americans by Wanda R. Harris MS, Walden University, 2013 MS, University of Southern Mississippi, 1996 BS, University of Southern Mississippi, 1992 Dissertation Submitted in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy Social Psychology
Clinical evolutional aspects of chronic subdural haematomas – literature review

Apparently trivial, one of the most frequent pathologies in neurosurgical practice, chronic subdural haematoma, continues to be a challenge for the neurosurgeons both from the therapeutic and postoperatory complications point of view, taking into account that it is frequently met in elders, who usually present a complex pathology. The fact that, by definition, there is a latent period between the moment the brain injury, usually minor, occurs and the appearance of clinical symptomatology, frequently makes the trauma be ignored, this complicating the diagnosis and most of the times delaying the application of the adequate treatment. Developing slowly in time, in weeks or months, the aspect that chronic subdural haematoma usually occurs in elders should not be neglected, its clinical symptomatology often debuting with memory and attention disorders, so that the patient is usually referred to psychiatrists or neurologists, only a paraclinical investigation (CT scan or MRI) being able to establish the diagnosis. Even the appearance of the lateral signs is subjected to many diagnosis confusions because patients deny the existence of a trauma in over 50% of the cases. Abbreviations: CT = computed tomography, MRI = magnetic resonance imaging, CSDH = chronic subdural haematoma, HMW = high molecular weight, F = frontal, T = temporal, P = parietal
Coadaptation in mother and infant regulated by a paternally expressed imprinted gene

This study investigates how a targeted mutation of a paternally expressed imprinted gene regulates multiple aspects of foetal and post–natal development including placental size, foetal growth, suckling and post–natal growth, weaning age and puberty onset. This same mutation in a mother impairs maternal reproductive success with reduced maternal care, reduced maternal food intake during pregnancy, and impaired milk let–down, which in turn reduces infant growth and delays weaning and onset of puberty. The significance of these coadaptive traits being synchronized in mother and offspring by the same paternally expressed imprinted gene ensures that offspring that have extracted ‘good’ maternal nurturing will themselves be both well provisioned and genetically predisposed towards ‘good’ mothering.
Impact of a mindfulness intervention on perceived stress, depression, and anxiety in college students

Rates of anxiety and depression are increasing in young adults and college students (D’Amico, Mechling, Kemppainen, Ahem, & Lee, 2016). College is a time that can be filled with academic, financial, personal, and identity stressors. One potential way that college students can cope with perceived stress is through mindfulness. This current study examined the relationship between mindfulness, perceived stress, anxiety, and depression in college students. More specifically this study examined differences in these measures over the course of a semester in a mindfulness and yoga based stress management and wellness class, a stress management class that did not receive a mindfulness intervention, and a general health class, that was a component to the university’s general education program. We predicted that a mindfulness intervention in the context of a stress management class would significantly reduce levels of stress, depression as operationalized by demoralization and anhedonia, and anxiety over the course of a semester when compared to a general stress management and wellness class and a general health class. We also predicted that both stress management and wellness classes would be significantly different from the general health class on these measures. It was hypothesized that the mindfulness and yoga based stress management and wellness class would be significantly higher on measures of mindfulness than the other groups. The Perceived Stress Scale, the Minnesota Behavioral Health Screener, and the Five-Facet Mindfulness Questionnaire were used in a multivariate analysis of variance (MANOVA). However, there were no statistically significant differences between the groups on perceived stress, demoralization, anhedonia, and anxiety.