Miracle-dz/UniFAR-FTUs huggingface dataset:
Effects of stream flow patterns on riparian vegetation of a semiarid river: Implications for a changing climate

As global climate change affects recharge and runoff processes, stream flow regimes are being altered. In the American Southwest, increasing aridity is predicted to cause declines in stream base flows and water tables. Another potential outcome of climate change is increased flood intensity. Changes in these stream flow conditions may independently affect vegetation or may have synergistic effects. Our goal was to extrapolate vegetation response to climate‐linked stream flow changes, by taking advantage of the spatial variation in flow conditions over a 200 km length of the San Pedro River (Arizona). Riparian vegetation traits were contrasted between sites differing in low‐flow hydrology (degree of stream intermittency) and flood intensity (stream power of the 10‐year recurrence flood). Field data indicate that increased stream intermittency would cause the floodplain plant community to shift from hydric pioneer trees and shrubs (Populus, Salix, Baccharis) towards mesic species (Tamarix). This shift in functional type would produce changes in vegetation structure, with reduced canopy cover and shorter canopies at drier sites. Among herbaceous species, annuals would increase while perennials would decrease. If flood intensities increased, there would be shifts towards younger tree age, expansion of xeric pioneer shrubs (in response to flood‐linked edaphic changes), and replacement of herbaceous perennials by annuals. Woody stem density would increase and basal area would decrease, reflecting shifts towards younger forests. Some effects would be compounded: Annuals were most prevalent, and tree canopies shortest, at sites that were dry and intensely flooded. Vegetational changes would feedback onto hydrologic and geomorphic processes, of importance for modeling. Increased flood intensity would have positive feedback on disturbance processes, by shifting plant communities towards species with less ability to stabilize sediments. Feedbacks between riparian vegetation and stream low‐flow changes would be homeostatic, with reduced evapotranspiration rates ameliorating declines in base flows arising from increased aridity. Copyright © 2009 John Wiley & Sons, Ltd.
Pricing exotic options using improved strong convergence

Today, better numerical approximations are required for multi-dimensional SDEs to improve on the poor performance of the standard Monte Carlo integration. With this aim in mind, the material in the thesis is divided into two main categories, stochastic calculus and mathematical finance. In the former, we introduce a new scheme or discrete time approximation based on an idea of Paul Malliavin where, for some conditions, a better strong convergence order is obtained than the standard Milstein scheme without the expensive simulation of the Levy Area. We demonstrate when the conditions of the 2−Dimensional problem permit this and give an exact solution for the orthogonal transformation (θ Scheme or Orthogonal Milstein Scheme). Our applications are focused on continuous time diffusion models for the volatility and variance with their discrete time approximations (ARV). Two theorems that measure with confidence the order of strong and weak convergence of schemes without an exact solution or expectation of the system are formally proved and tested with numerical examples. In addition, some methods for simulating the double integrals or Levy Area in the Milstein approximation are introduced. For mathematical finance, we review evidence of non-constant volatility and consider the implications for option pricing using stochastic volatility models. A general stochastic volatility model that represents most of the stochastic volatility models that are outlined in the literature is proposed. This was necessary in order to both study and understand the option price properties. The analytic closed-form solution for a European/Digital option for both the Square Root Model and the 3/2 Model are given. We present the Multilevel Monte Carlo path simulation method which is a powerful tool for pricing exotic options. An improved/updated version of the ML-MC algorithm using multi-schemes and a non-zero starting level is introduced. To link the contents of the thesis, we present a wide variety of pricing exotic option examples where considerable computational savings are demonstrated using the new θ Scheme and the improved Multischeme Multilevel Monte Carlo method (MSL-MC). The computational cost to achieve an accuracy of O(e) is reduced from O(e−3) to O(e−2) for some applications.
SNARE priming is essential for maturation of autophagosomes but not for their formation

Significance The contribution of SNARE-mediated membrane fusion to the different stages along the autophagic process is not well understood. In this work we demonstrate that inhibition of SNARE priming leads to impairment of the autophagic flux manifested by the accumulation of mature autophagosomes that do not fuse with the lysosomes. Our results suggest that SNARE priming is essential for the fusion of the autophagosome with the lysosome but not for autophagosome formation. Autophagy, a unique intracellular membrane-trafficking pathway, is initiated by the formation of an isolation membrane (phagophore) that engulfs cytoplasmic constituents, leading to generation of the autophagosome, a double-membrane vesicle, which is targeted to the lysosome. The outer autophagosomal membrane consequently fuses with the lysosomal membrane. Multiple membrane-fusion events mediated by SNARE molecules have been postulated to promote autophagy. αSNAP, the adaptor molecule for the SNARE-priming enzyme N-ethylmaleimide-sensitive factor (NSF) is known to be crucial for intracellular membrane fusion processes, but its role in autophagy remains unclear. Here we demonstrated that knockdown of αSNAP leads to inhibition of autophagy, manifested by an accumulation of sealed autophagosomes located in close proximity to lysosomes but not fused with them. Under these conditions, moreover, association of both Atg9 and the autophagy-related SNARE protein syntaxin17 with the autophagosome remained unaffected. Finally, our results suggested that under starvation conditions, the levels of αSNAP, although low, are nevertheless sufficient to partially promote the SNARE priming required for autophagy. Taken together, these findings indicate that while autophagosomal–lysosomal membrane fusion is sensitive to inhibition of SNARE priming, the initial stages of autophagosome biogenesis and autophagosome expansion remain resistant to its loss.
Hankel Transforms of Linear Combinations of Catalan Numbers

Cvetkovic, Rajkovic, and Ivkovic proved that the Hankel transform of the sequence of sums of adjacent Catalan numbers is the bisection of the sequence of Fibonacci num- bers. Here, we find recurrence relations for the Hankel transform of more general linear combinations of Catalan numbers, involving up to four adjacent Catalan numbers, with arbitrary coefficients. Using these, we make certain conjectures about the recurrence relations satisfied by the Hankel transform of more extended linear combinations.
Evolutionarily labile responses to a signal of aggressive intent

Males of many swordtail species possess vertical bar pigment patterns that are used both in courtship and agonistic interactions. Expression of the bars may function as a conventional threat signal during conflicts with rival males; bars intensify at the onset of aggression and fade in the subordinate male at contest's end. We used mirror image stimulation and bar manipulations to compare the aggressive responses of the males of four swordtail species to their barred and barless images. We found that having a response to the bars is tightly linked to having genes for bars, while the nature of the response the bars evoked varied across species. Specifically, we report the first known instance where closely related species exhibited differing and contradictory responses to a signal of aggressive motivation. Demonstrating that a signal conveys the same information across species (aggressive intent) while the response to that information has changed among species suggests that the nature of the responses are more evolutionarily labile than the signal.
FTY720 Induces Apoptosis of M2 Subtype Acute Myeloid Leukemia Cells by Targeting Sphingolipid Metabolism and Increasing Endogenous Ceramide Levels

The M2 subtype Acute Myeloid Leukemia (AML-M2) with t(8;21) represents an unmet challenge because of poor clinical outcomes in a sizable portion of patients. In this study,we report that FTY720 (Fingolimod), a sphingosine analogue and an FDA approved drug for treating of multiple sclerosis, shows antitumorigenic activity against the Kasumi-1 cell line, xenograft mouse models and leukemic blasts isolated from AML-M2 patients with t(8;21) translocation. Primary investigation indicated that FTY720 caused cell apoptosis through caspases and protein phosphatase 2A (PP2A) activation. Transcriptomic profiling further revealed that FTY720 treatment could upregulate AML1 target genes and interfere with genes involved in ceramide synthesis. Treatment with FTY720 led to the elimination of AML1-ETO oncoprotein and caused cell cycle arrest. More importantly, FTY720 treatment resulted in rapid and significant increase of pro-apoptotic ceramide levels, determined by high-performance liquid chromatography-electrospray ionization tandem mass spectrometry based lipidomic approaches. Structural simulation model had also indicated that the direct binding of ceramide to inhibitor 2 of PP2A (I2PP2A) could reactivate PP2A and cause cell death. This study demonstrates, for the first time, that accumulation of ceramide plays a central role in FTY720 induced cell death of AML-M2 with t(8;21). Targeting sphingolipid metabolism by using FTY720 may provide novel insight for the drug development of treatment for AML-M2 leukemia.
Thermal Desorption Remediation of Soil Highly Polluted by 1,2-Dichloroethane in China

A full-field investigation was conducted of thermal desorption remediation of soil polluted by 1, 2-dichloroethane (1, 2-DCA). The effects of soil type, system temperature, thermal desorption time, and stirring speed on the residual concentration of 1, 2-DCA were determined. The residual concentration of 1, 2-DCA decreased with increasing viscosity, system temperature, thermal desorption time, and stirring speed. Optimal thermal desorption conditions for moderately polluted clay soil were a system temperature of 130°C and thermal desorption time of 50 min with stirring. Optimal thermal desorption conditions for heavily polluted clay soil were a system temperature of 130°C and thermal desorption time of 90 min with stirring. This study provides technological parameters and theoretical guidance for engineering.
Multi-User Massive MIMO Communication Systems Based on Irregular Antenna Arrays

In practical mobile communication engineering applications, surfaces of antenna array deployment regions are usually uneven. Therefore, massive multi-input-multi-output (MIMO) communication systems usually transmit wireless signals by irregular antenna arrays. To evaluate the performance of irregular antenna arrays, the matrix correlation coefficient and the ergodic received gain are defined for massive MIMO communication systems with mutual coupling effects. Furthermore, the lower bound of the ergodic achievable rate, symbol error rate, and average outage probability is first derived for multi-user massive MIMO communication systems using irregular antenna arrays. Asymptotic results are also derived when the number of antennae approaches infinity. Numerical results indicate that there exists a maximum achievable rate when the number of antennae keeps increasing in massive MIMO communication systems using irregular antenna arrays. Moreover, the irregular antenna array outperforms the regular antenna array in the achievable rate of massive MIMO communication systems when the number of antennae is larger than or equal to a given threshold.
Profile of pridopidine and its potential in the treatment of Huntington disease: the evidence to date

Huntington disease (HD) is a chronic, genetic, neurodegenerative disease for which there is no cure. The main symptoms of HD are abnormal involuntary movements (chorea and dystonia), impaired voluntary movements (ie, incoordination and gait balance), progressive cognitive decline, and psychiatric disturbances. HD is caused by a CAG-repeat expanded mutation in the HTT gene, which encodes the huntingtin protein. The inherited mutation results in the production of an elongated polyQ mutant huntingtin protein (mHtt). The cellular functions of the Htt protein are not yet fully understood, but the functions of its mutant variant are thought to include alteration of gene transcription and energy production, and dysregulation of neurotransmitter metabolism, receptors, and growth factors. The phenylpiperidines pridopidine (4-[3-methanesulfonyl-phenyl]-1-propyl-piperidine; formerly known as ACR16) and OSU6162 ([S]-[-]-3-[3-methane [sulfonyl-phenyl]-1-propyl-piperidine) are members of a new class of pharmacologic agents known as “dopamine stabilizers”. Recent clinical trials have highlighted the potential of pridopidine for symptomatic treatment of patients with HD. More recently, the analysis of HD models (ie, in vitro and in mice) highlighted previously unknown effects of pridopidine (increase in brain-derived neurotrophic factor, reduction in mHtt levels, and σ-1 receptor binding and modulation). These additional functions of pridopidine suggest it might be a neuroprotective and disease-modifying drug. Data from ongoing clinical trials of pridopidine will help define its place in the treatment of HD. This commentary examines the available preclinical and clinical evidence regarding the use of pridopidine in HD.
The 1.25 A resolution refinement of the cholera toxin B-pentamer: evidence of peptide backbone strain at the receptor-binding site.

Crystals of the 61 kDa complex of the cholera toxin B-pentamer with the ganglioside GM1 receptor pentasaccharide diffract to near-atomic resolution. We have refined the crystallographic model for this complex using anisotropic displacement parameters for all atoms to a conventional crystallographic residual R=0.129 for all observed Bragg reflections in the resolution range 22 A to 1.25 A. Remarkably few residues show evidence of discrete conformational disorder. A notable exception is a minority conformation found for the Cys9 side-chain, which implies that the Cys9-Cys86 disulfide linkage is incompletely formed. In all five crystallographically independent instances, the peptide backbone in the region of the receptor-binding site shows evidence of strain, including unusual bond lengths and angles, and a highly non-planar (omega=153.7(7) degrees) peptide group between residues Gln49 and Val50. The location of well-ordered water molecules at the protein surface is notable reproduced among the five crystallographically independent copies of the peptide chain, both at the receptor-binding site and elsewhere. The 5-fold non-crystallographic symmetry of this complex allows an evaluation of the accuracy, reproducibility, and derived error estimates from refinement of large structures at near-atomic resolution. We find that blocked-matrix treatment of parameter covariance underestimates the uncertainty of atomic positions in the final model by approximately 10% relative to estimates based either on full-matrix inversion or on the 5-fold non-crystallographic symmetry.
Reproducibility and sensitivity of muscle reoxygenation and oxygen uptake recovery kinetics following running exercise in the field

The purpose of this study was to assess the reliability of postexercise near‐infrared spectroscopy (NIRS)‐derived measurements and their sensitivity to different exercise intensities in the field. Seventeen athletes (24·1 ± 5·6 year) repeated, on three occasions, two 2‐min submaximal shuttle‐runs at 40% and 60% of VIFT (final speed of the 30–15 intermittent fitness test) and a 50‐m shuttle‐run sprint (Sprint), with (OCC) or without (CON) repeated transient arterial occlusions of the medial gastrocnemius during the postexercise period. NIRS variables (i.e. oxyhaemoglobin [HbO2], deoxyhaemoglobin [HHb] and their difference [Hbdiff]) were measured continuously for 3 min after each exercise. Half‐recovery (½Rec) and mean response (MRT; monoexponential curve fitting) times of muscle reoxygenation and muscle oxygen uptake () recovery were calculated. Reliability was assessed using the typical error of measurement, expressed as a coefficient of variation (CV). Postexercise recovery of muscle reoxygenation revealed CVs ranging from 16·8% to 37·3%; CV for recovery ranged from 6·2% to 20·9%, with no substantial differences shown between NIRS variables and exercise intensities. While running, intensity did not affect MRT or ½Rec for muscle reoxygenation, and differences were found for recovery (e.g. [Hbdiff]‐ MRT = 28·7 ± 5·2, 34·2 ± 5·1 and 37·3 ± 6·2 s for 40%, 60% and Sprint, respectively, P<0·01). To conclude, the kinetics of postexercise NIRS measurements showed CV values ranging from 6% to 37%, with no substantial differences between exercise intensities or NIRS‐derived variables. However, exercise intensity did influence recovery kinetics, but not that of muscle reoxygenation in an occlusion‐free condition.
Neisseria meningitidis serogroup W135 isolates associated with the ET-37 complex.

To the Editor: As of April 20, 2000, >300 laboratory confirmed cases of meningococcal disease caused by N. meningitidis serogroup W135 (NMW135) have been reported in Saudi Arabia and nine other countries among Hajj pilgrims or their close contacts (1). This is the first reported multinational outbreak of W135 meningococcal disease. NMW135 accounts for <5% of meningococcal disease in the United States and worldwide. The main cause of meningococcal disease outbreaks, especially in the African " meningitis belt, " which extends from Ethiopia in the east to Senegal in the west, has long been N. meningitidis serogroup A. An epidemic, caused by a particular clonal group of serogroup A, identified by multilocus enzyme electrophoresis (MEE) as subgroup (2) and may have caused earlier epidemics in China. In 1987, an outbreak of group A meningococcal disease caused by the same clonal group occurred in association with the annual Moslem pilgrimage to Mecca (Hajj) (3). At that time, Saudi Arabia implemented vaccination requirements for all entering pilgrims. The vaccine formulations vary; bivalent A/C vaccine or quadrivalent A/C/ Y/W135 vaccine (as licensed in the United States) is used. We present molecular characterization results of NMW135 isolates from four U.S. patients with meningococcal disease. These cases were epidemiologically linked to this year's Hajj in Saudi Arabia, which concluded on March 17, 2000 (4). We examine the origin and potential relatedness of the NMW135 isolates to some of the major N. meningitidis virulent clones. Two patients (both vaccinated with quadrivalent A/C/Y/W135 vaccine) were returning pilgrims; one was a close household contact of another pilgrim, the other had other possible contacts with the U.S. pilgrims. Three isolates were identified as NMW135 at the New York City Health Department and the fourth at the California Department of Health. Serogroup identification was confirmed at the Centers for Disease Control and Prevention (CDC) by standard microbiologic methods (5). MEE has long been the standard method for molecular subtyping of N. meningitidis and has allowed identification of several major epidemic prone clones. When the MEE system established by Caugant et al. (6) and that used at CDC were recently compared, they demonstrated excellent correlation segregating individual electrophoretic types (ETs) into similar clusters. A virulent clone, designated ET-37 complex, which contains >50 different ETs, is mainly composed of N. meningitidis serogroup C. In the United States, strains of ET-24 (within the ET-37 complex) are the main cause of meningococcal disease outbreaks …
The Role of Cancer-Testis Antigens as Predictive and Prognostic Markers in Non-Small Cell Lung Cancer

Background Cancer-Testis Antigens (CTAs) are immunogenic proteins that are poor prognostic markers in non-small cell lung cancer (NSCLC). We investigated expression of CTAs in NSCLC and their association with response to chemotherapy, genetic mutations and survival. Methods We studied 199 patients with pathological N2 NSCLC treated with neoadjuvant chemotherapy (NAC; n = 94), post-operative observation (n = 49), adjuvant chemotherapy (n = 47) or unknown (n = 9). Immunohistochemistry for NY-ESO-1, MAGE-A and MAGE-C1 was performed. Clinicopathological features, response to neoadjuvant treatment and overall survival were correlated. DNA mutations were characterized using the Sequenom Oncocarta panel v1.0. Affymetrix data from the JBR.10 adjuvant chemotherapy study were obtained from a public repository, normalised and mapped for CTAs. Results NY-ESO-1 was expressed in 50/199 (25%) samples. Expression of NY-ESO-1 in the NAC cohort was associated with significantly increased response rates (P = 0.03), but not overall survival. In the post-operative cohort, multivariate analyses identified NY-ESO-1 as an independent poor prognostic marker for those not treated with chemotherapy (HR 2.61, 95% CI 1.28–5.33; P = 0.008), whereas treatment with chemotherapy and expression of NY-ESO-1 was an independent predictor of improved survival (HR 0.267, 95% CI 0.07–0.980; P = 0.046). Similar findings for MAGE-A were seen, but did not meet statistical significance. Independent gene expression data from the JBR.10 dataset support these findings but were underpowered to demonstrate significant differences. There was no association between oncogenic mutations and CTA expression. Conclusions NY-ESO-1 was predictive of increased response to neoadjuvant chemotherapy and benefit from adjuvant chemotherapy. Further studies investigating the relationship between these findings and immune mechanisms are warranted.
Rice consumption and cancer incidence in US men and women

While both the 2012 and 2014 Consumer Reports concerned arsenic levels in US rice, no previous study has evaluated long‐term consumption of total rice, white rice and brown rice in relation to risk of developing cancers. We investigated this in the female Nurses' Health Study (1984–2010), and Nurses' Health Study II (1989–2009), and the male Health Professionals Follow‐up Study (1986–2008), which included a total of 45,231 men and 160,408 women, free of cancer at baseline. Validated food frequency questionnaires were used to measure rice consumption at baseline and repeated almost every 4 years thereafter. We employed Cox proportional hazards regression model to estimate multivariable relative risks (RRs) and 95% confidence intervals (95% CIs). During up to 26 years of follow‐up, we documented 31,655 incident cancer cases (10,833 in men and 20,822 in women). Age‐adjusted results were similar to multivariable‐adjusted results. Compared to participants with less than one serving per week, the multivariable RRs of overall cancer for individuals who ate at least five servings per week were 0.97 for total rice (95% CI: 0.85–1.07), 0.87 for white rice (95% CI: 0.75–1.01), and 1.17 for brown rice (95% CI: 0.90–1.26). Similar non‐significant associations were observed for specific sites of cancers including prostate, breast, colon and rectum, melanoma, bladder, kidney, and lung. Additionally, the null associations were observed among European Americans and non‐smokers, and were not modified by BMI. Long‐term consumption of total rice, white rice or brown rice was not associated with risk of developing cancer in US men and women.