Miracle-dz/UniFAR-FTUs huggingface dataset:
The influence of drought on the fish and invertebrate populations of an upland stream in Wales

SUMMARY. 1. The exceptionally dry summer of 1976 presented an opportunity to assess the impact of drought on the fauna of an unregulated stream in Wales. 2. Total number of macroinvertebrates varied from 1808 m−2 in September 1976 to 7412m−2 in August 1977. Two main effects of drought were observed: an initial reduction in abundance during the drought and a change in community structure in the following year, probably through impaired reproduction. 3. Trout density ranged from 0.075±0.028 to 0.402±0.093 m−2 and salmon parr density varied between 0.014±0.004 and 0.414±0.119 m−2. The only detrimental effect of the drought on the fish fauna was the elimination of the 1976 year class of young salmon. probably due to prolonged high water temperature.
Compilation and Code Optimization for Data Analytics

The trade-offs between the use of modern high-level and low-level programming languages in constructing complex software artifacts are well known. High-level languages allow for greater programmer productivity: abstraction and genericity allow for the same functionality to be implemented with significantly less code compared to low-level languages. Modularity, object-orientation, functional programming, and powerful type systems allow programmers not only to create clean abstractions and protect them from leaking, but also to define code units that are reusable and easily composable, and software architectures that are adaptable and extensible. The abstraction, succinctness, and modularity of high-level code help to avoid software bugs and facilitate debugging and maintenance. The use of high-level languages comes at a performance cost: increased indirection due to abstraction, virtualization, and interpretation, and superfluous work, particularly in the form of tempory memory allocation and deallocation to support objects and encapsulation. As a result of this, the cost of high-level languages for performance-critical systems may seem prohibitive. The vision of abstraction without regret argues that it is possible to use high-level languages for building performance-critical systems that allow for both productivity and high performance, instead of trading off the former for the latter. In this thesis, we realize this vision for building different types of data analytics systems. Our means of achieving this is by employing compilation. The goal is to compile away expensive language features – to compile high-level code down to efficient low-level code.
Advances in Therapeutic Targeting of Cancer Stem Cells within the Tumor Microenvironment: An Updated Review

Despite great strides being achieved in improving cancer patients’ outcomes through better therapies and combinatorial treatment, several hurdles still remain due to therapy resistance, cancer recurrence and metastasis. Drug resistance culminating in relapse continues to be associated with fatal disease. The cancer stem cell theory posits that tumors are driven by specialized cancer cells called cancer stem cells (CSCs). CSCs are a subpopulation of cancer cells known to be resistant to therapy and cause metastasis. Whilst the debate on whether CSCs are the origins of the primary tumor rages on, CSCs have been further characterized in many cancers with data illustrating that CSCs display great abilities to self-renew, resist therapies due to enhanced epithelial to mesenchymal (EMT) properties, enhanced expression of ATP-binding cassette (ABC) membrane transporters, activation of several survival signaling pathways and increased immune evasion as well as DNA repair mechanisms. CSCs also display great heterogeneity with the consequential lack of specific CSC markers presenting a great challenge to their targeting. In this updated review we revisit CSCs within the tumor microenvironment (TME) and present novel treatment strategies targeting CSCs. These promising strategies include targeting CSCs-specific properties using small molecule inhibitors, immunotherapy, microRNA mediated inhibitors, epigenetic methods as well as targeting CSC niche-microenvironmental factors and differentiation. Lastly, we present recent clinical trials undertaken to try to turn the tide against cancer by targeting CSC-associated drug resistance and metastasis.
Oxazoles : synthesis, reactions, and spectroscopy

Abbreviations.1. Synthesis and Reactions of Oxazoles (D.C. Palmer and S. Venkatraman). 2. Spectroscopic Properties of Oxazoles (D. Lowe). 3. Oxazole Diels-Alder Reactions (J.I. Levin and L.M. Laakso). 4. Mesoionic Oxazoles (G.W. Gribble). Author Index.Subject Index.
REPLY TO COMMENTS BY REVIEWER #1

The statement that ice mass density agrees with ice water content doesn’t make sense since these are two totally different quantities (one is the other integrated in the vertical). Of course, when reading the full text it is clear that the authors mean that the two properties are consistent with each other after properly accounting for the vertical extent of the cloud and integrating the limb observations in the vertical. Please clarify Reply: Good point. We replaced the text section: “We find that the primary OSIRIS tomography product, cloud scattering coefficient, shows very good agreement with the primary CIPS product, cloud albedo with a correlation coefficient of 0.96. However, OSIRIS systematically reports brighter clouds than CIPS and the bias between the instruments (OSIRIS CIPS) is 3.4e-6 sr (±2.9e-6 sr) on average. The OSIRIS tomography ice mass density agrees well with the CIPS ice water content, with a correlation coefficient of 0.91. “ With the following text section: “We find that the OSIRIS albedo (obtained from the vertical integration of the cloud scattering coefficient) shows very good agreement with the primary CIPS product, cloud albedo with a correlation coefficient of 0.96. However, OSIRIS systematically reports brighter clouds than CIPS and the bias between the instruments (OSIRIS CIPS) is 3.4e-6 sr (±2.9e-6 sr) on average. The OSIRIS tomography ice water content (obtained from the vertical integration of ice mass density) agrees well with the CIPS ice water content, with a correlation coefficient of 0.91. ” Page 1, line 35: Gadsden and Schröder is a nice textbook but certainly not an original scientific reference. Please replace with suitable references of original measurements (e.g., Lübken, 1999 and/or some even older papers from the Stockholm group based on rocket grenade measurements). Reply: This has been corrected, the reference Gadsden and Schröder has been replaced by Lübken, 1999. Page 2, line 4: When referring to these initial observations reference should also be made to the paper by Jesse, 1885: Jesse, O. , Auffallende Erscheinungen am Abendhimmel, Met. Zeit. , 2, 311-312, 1885. Reply: The reference (Jesse, 1885) has been added. Page 2, line 8: Please add "e.g.," in front of the reference to the paper by Fritts et al., 1993. Reply: This has been added. Page 2, line 9: At the end of the sentence after the reference above, I would add a reference to the classical paper by Witt, 1962: Witt, G. , Height, structure and displacements of noctilucent clouds, Tellus XIV , 1 , 1-18, 1962. Reply: Reference added. Page 2, line 22: typo "ferquency"
Double-diffusive instabilities at a vertical sidewall after the sudden onset of heating

Abstract When body of fluid with a salinity gradient is heated from an isolated vertical wall instabilities can form. These have been observed in many experiments. The evolving temperature boundary layer causes the fluid to rise and generates horizontal salinity gradients and vertical shear. These background temperature and salinity gradients and the shear can all drive (or inhibit) the instabilities. The time-dependent nature of the background gradients has previously restricted linear stability analysis to some limits where a quasi-static assumption could be made. However, in many of the experiments this assumption is not valid. We investigate the instabilities over the full range of salinity gradients and applied heating, from what is essentially the thermal problem to the strong salinity gradient limit, with two different heating rates. The approach taken is to find the optimal evolution of a quadratic energy-like measure of the amplitude of the instabilities as the background state evolves. This involves a matrix optimization problem. The choice of quadratic measure is not predetermined, but selected to minimize this optimal growth. This approach has been developed previously for the purely thermal case of heating from isolated horizontal and vertical boundaries, and to the double-diffusive problem of heating a salinity gradient from a horizontal lower boundary. We show that there are three regimes of instability when a salinity gradient is heated from a sidewall. There are the small and large Prandtl number regimes observed previously in the purely thermal problem. As the salinity gradient increases the shear-driven small Prandtl number mode is suppressed and only the large Prandtl number mode is observed. For larger salinity gradients a double-diffusive mode of instability appears, which initially has an order-one aspect ratio. As the salinity gradient further increases it evolves into the thin almost horizontal intrusions of the quasi-static analysis. These findings are in line with experimental observations.
Universally valid reduction of multiscale stochastic biochemical systems using simple non-elementary propensities

Biochemical systems consist of numerous elementary reactions governed by the law of mass action. However, experimentally characterizing all the elementary reactions is nearly impossible. Thus, over a century, their deterministic models that typically contain rapid reversible bindings have been simplified with non-elementary reaction functions (e.g., Michaelis-Menten and Morrison equations). Although the non-elementary reaction functions are derived by applying the quasi-steady-state approximation (QSSA) to deterministic systems, they have also been widely used to derive propensities for stochastic simulations due to computational efficiency and simplicity. However, the validity condition for this heuristic approach has not been identified even for the reversible binding between molecules, such as protein-DNA, enzyme-substrate, and receptor-ligand, which is the basis for living cells. Here, we find that the non-elementary propensities based on the deterministic total QSSA can accurately capture the stochastic dynamics of the reversible binding in general. However, serious errors occur when reactant molecules with similar levels tightly bind, unlike deterministic systems. In that case, the non-elementary propensities distort the stochastic dynamics of a bistable switch in the cell cycle and an oscillator in the circadian clock. Accordingly, we derive alternative non-elementary propensities with the stochastic low-state QSSA, developed in this study. This provides a universally valid framework for simplifying multiscale stochastic biochemical systems with rapid reversible bindings, critical for efficient stochastic simulations of cell signaling and gene regulation. To facilitate the framework, we provide a user-friendly open-source computational package, ASSISTER, that automatically performs the present framework.
Phonology and Phonetics of L2 Telugu English

The paper provides a partial phonological and phonetic description of the segmental structure of L2 Telugu English (TE). Previous research on the subject has been carried out in the context of a more general notion of Indian English (IE), so the properties of TE as distinct from other varieties of IE (e.g., Gujarati English) have largely remained unexplored. We have primarily focused on areas that previous research identified as prominent issues in the study of IE: vowel inventory and production, representation and realization of liquids, word-final obstruent phenomena, and allophones of /w/. To account for these aspects of TE, we have combined a generative approach to the study of an individual’s linguistic competence with linguistic fieldwork as a means of collecting first-hand data. On the basis of collected data, we have conducted a spectrographic analysis of TE vowels and a distributional analysis of TE consonants. The paper provides the first description of the acoustic spaces of TE vowels. We found that all vowels except [? ] and [i] are more central in TE than in General American English. /r/ was realized as either [r] or [? ] without a specific pattern, and occasionally as [? ] in the intervocalic position. /l/ was realized as [? ] in word-final position and as [l] elsewhere. TE displayed word-final obstruent devoicing for all obstruents except for /b/, which was consistently unreleased. /w/ was realized as [? ] before front vowels and as [w] elsewhere. While previous research that concentrated on the broad notion of Indian English recognized the issue of /w/-allophony, it has not provided a principle that governs the exact distribution of /w/’s allophones. By combining the generative framework with linguistic fieldwork, we have accounted for this long-standing puzzle with a single rule: /w/ ? [? ] / __ [–CONS, –BACK] .
Multicolor Size-Ramsey Number of Cycles

Given a positive integer $ r $, the $ r $-color size-Ramsey number of a graph $ H $, denoted by $ \hat{R}(H, r) $, is the smallest integer $ m $ for which there exists a graph $ G $ with $ m $ edges such that, in any edge coloring of $ G $ with $ r $ colors, $G$ contains a monochromatic copy of $ H $. Haxell, Kohayakawa and \L uczak showed that the size-Ramsey number of a cycle $ C_n $ is linear in $ n $ i.e. $ \hat{R}(C_n, r) \leq c_rn $, for some constant $ c_r $. Their proof, however, is based on the Szemer\'edi's regularity lemma and so no specific constant $ c_r $ is known. Javadi, Khoeini, Omidi and Pokrovskiy gave an alternative proof for this result which avoids using of the regularity lemma. Indeed, they proved that if $ n $ is even, then $ c_r $ is exponential in $ r $ and if $ n $ is odd, then $ c_r $ is doubly exponential in $ r $. \noindent In this paper, we improve the bound $c_r$ and prove that $c_r$ is polynomial in $r$ when $n$ is even and is exponential in $r$ when $n$ is odd. We also prove that in the latter case, it cannot be improved to a polynomial bound in $r$. More precisely, we prove that there are some positive constants $c_1,c_2$ such that for every even integer $n$, we have $c_1r^2n\leq \hat{R}(C_n,r)\leq c_2r^{120}(\log^2 r)n$ and for every odd integer $n$, we have $c_1 2^{r}n \leq \hat{R}(C_n, r)\leq c_22^{16 r^2+2\log r}n $.
Social norms of college students engaging in non-medical prescription drug use to get high: What’s sex got to do with it?

Abstract Background: Relationships exist between perceived peer and own use of alcohol, cannabis, and tobacco, particularly when peers and participants are sex-matched. We investigated sex influences on social norms effects for college students’ non-medical prescription drug use (NMPDU). Methods: N = 1986 college students reported on their perceptions of male and female peers’ NMPDU frequency and their own past-month NMPDU. Results: Approximately 3% of students self-reported past month NMPDU, with no sex differences. In a linear mixed model, participants who engaged in NMPDU perceived significantly more frequent peer use. Female participants perceived more frequent peer NMPDU than did male participants, particularly when perceiving male peers’ NMPDU. Significant positive correlations were found between perceived peer NMPDU frequency and participants’ own NMPDU for all peer-participant sex combinations, with no evidence for stronger correlations with sex-matched pairs. Conclusions: While social norm interventions may be effective for college student NMPDU, sex-matching of these interventions is likely unnecessary.
Effectiveness of Ginseng in Treating Erectile Dysfunction: A Review Paper

Early identification and treatment of erectile dysfunction (ED) and ED related comorbidities, including hypertension, diabetes mellitus, and hyperlipidemia is crucial in improving the quality of life of men and their partners. To date, the main treatment options for ED can be divided into pharmacological and surgical interventions. These treatments include oral phosphodiesterase type 5 (PDE5) inhibitors (sildenafil, tadalafil, vardenafil), intraurethral or intracavernosal alprostadil, vacuum devices and penile prosthesis. Although considerable advances have been made, there seems to be a high dropout rate of the above treatment due to cultural restrictions and taboos. Subsequently, these patients would seek herbal dietary supplements such as ginseng as an alternative. Even though several studies have proved that ginseng is ideal in treating ED, the published trials on humans were not robust, and there is a lack of exploration of subjective outcomes. This literature review aimed to synthesize and critically appraise clinical and scientific literature on the effects of ginseng in managing ED. In total, 7 studies were included and reviewed. It was concluded that ginseng is a feasible alternative to currently available practices in treating ED due to a significant improvement in International Index of Erectile Function (IIEF)-5 scores and its safety profile. There is a higher likelihood to consider ginseng as an alternative therapy if more studies with larger-scaled clinical trials and higher standards on the safety and efficacy of ginseng are conducted in the future.
Towards an automated computational pipeline to guide drug lead optimization

Author(s): Liu, Shuai | Advisor(s): Mobley, David | Abstract: Molecular dynamics (MD) simulations are a promising tool to guide drug lead optimization. But because these tools are applied prospectively in drug discovery, blind tests provide a key opportunity to validate these for real-world applications. I participated in the Statistical Assessment of Modeling of Proteins and Ligands (SAMPL) 3 blind test (chapter 1) in which I used different force fields to calculate hydration free energies and SAMPL4 (chapter 2) in which I analyzed pose prediction results from different groups using different computational tools. The results from these blind tests improve our understanding of the accuracy of current methods, allowing us to improve these methods. Large-scale applications of MD simulations to drug discovery have been few, partly because of the difficulty of planning and setting up the simulations. For example, alchemical relative free energy (RFE) calculations have relatively high accuracy in predicting differences in binding between drug lead compounds and new derivatives which are sought to improve binding potency. But setting up RFE calculations for large sets of compounds has required far too much manual intervention to be practical. I helped develop an algorithm, LOMAP (chapter3), to automatically plan and set up these calculations. Resulting applications indicated that it could successfully reduce the time of planning RFE calculations. But in this project, we assumed that relative free energy (RFE) calculations involving ring breaking will introduce substantial error, and we tried to avoid these calculations as much as possible. Later, we quantitatively calculated what these errors would be to confirm this (chapter4). Beside binding free energy calculations, MD simulations can also be used to predict solubilities. We used free energy calculations (chapter5) to calculate relative solubilities and compared the results with experiment and with results from more empirical chemical engineering methods. We found that our approach is more accurate, despite its straightforward nature. Long-term, we are working towards developing an automated pipeline to help guide key aspects of drug lead optimization. My work helped with understanding the accuracy of current techniques, improving their automation, and providing a new technique for predicting physical properties like solubilities.
Mechanical, viscoelastic, and flammability properties of polymer composites reinforced with novel Sirisha bark filler

Today is the era of advanced materials to resolve the issue due to ecological hazards. Research is being carried out to find the alternative of the existing materials with a low cost and eco-friendly nature. Polypropylene (PP) is one of the major commodity thermoplastics having wide applications worldwide. The neat PP is extremely sensitive to flame and therefore it is a challenging task for the researchers to reduce the flame sensitivity of PP composites for safe applications. Though the artificial flame retardant filler reduces the flame propagation, these are hazardous, costly, not environment friendly and, they reduce the mechanical strength of the polymer composites upon higher percentage loading. To overcome this difficulty, in this work, the novel natural Sirisha bark filler was reinforced to the coir fiber/PP hybrid composites to enhance the flame retardant and mechanical properties. The time to ignite (TTI) of the hybrid composites increased due to bark filler reinforcement in the composites and the flame spread reduced to zero. The impact strength of hybrid composites was found to be increased due to the strong interfacial adhesion of the bark filler with the PP matrix. The scanning electron microscope (SEM) micrographs revealed the well-defined grain boundaries of hybrid composites. The carbonaceous char coating over the surface of the hybrid composite was observed from the char morphology that acts as a hindrance to flame. The viscoelastic properties such as storage modulus, loss modulus, and loss tangent of the hybrid composites were studied by using dynamic mechanical analysis (DMA).
Stability and Existence of Noncanonical I-motif DNA Structures in Computer Simulations Based on Atomistic and Coarse-Grained Force Fields

Cytosine-rich DNA sequences are able to fold into noncanonical structures, in which semi-protonated cytosine pairs develop extra hydrogen bonds, and these bonds are responsible for the overall stability of a structure called the i-motif. The i-motif can be formed in many regions of the genome, but the most representative is the telomeric region in which the CCCTAA sequences are repeated thousands of times. The ability to reverse folding/unfolding in response to pH change makes the above sequence and i-motif very promising components of nanomachines, extended DNA structures, and drug carriers. Molecular dynamics analysis of such structures is highly beneficial due to direct insights into the microscopic structure of the considered systems. We show that Amber force fields for DNA predict the stability of the i-motif over a long timescale; however, these force fields are not able to predict folding of the cytosine-rich sequences into the i-motif. The reason is the kinetic partitioning of the folding process, which makes the transitions between various intermediates too time-consuming in atomistic force field representation. Application of coarse-grained force fields usually highly accelerates complex structural transitions. We, however, found that three of the most popular coarse-grained force fields for DNA (oxDNA, 3SPN, and Martini) were not able to predict the stability of the i-motif structure. Obviously, they were not able to accelerate the folding of unfolded states into an i-motif. This observation must be strongly highlighted, and the need to develop suitable extensions of coarse-grained force fields for DNA is pointed out. However, it will take a great deal of effort to successfully solve these problems.