Miracle-dz/UniFAR-FTUs huggingface dataset:
Protein Denaturation, Zero Entropy Temperature, and the Structure of Water around Hydrophobic and Amphiphilic Solutes.

The hydrophobic effect plays a key role in many chemical and biological processes, including protein folding. Nonetheless, a comprehensive picture of the effect of temperature on hydrophobic hydration and protein denaturation remains elusive. Here, we study the effect of temperature on the hydration of model hydrophobic and amphiphilic solutes, through molecular dynamics, aiming at getting insight on the singular behavior of water, concerning the zero-entropy temperature, TS, and entropy convergence, TS*, also observed for some proteins, upon denaturation. We show that, similar to hydrocarbons, polar amphiphilic solutes exhibit a TS, although strongly dependent on solute-water interactions, opposite to hydrocarbons. Further, the temperature dependence of the hydration entropy, normalized by the solvent accessible surface area, is shown to be nearly solute size independent for hydrophobic but not for amphiphilic solutes, for similar reasons. These results are further discussed in the light of information theory (IT) and the structure of water around hydrophobic groups. The latter shows that the tetrahedral enhancement of some water molecules around hydrophobic groups, associated with the reduction of water defects, leads to the strengthening of the weakest hydrogen bonds, relative to bulk water. In addition, a larger tetrahedrality is found in low density water populations, demonstrating that pure water has encoded structural information, similar to that associated with hydrophobic hydration. The reversal of the hydration entropy dependence on the solute size, above TS*, is also analyzed and shown to be associated with a greater loss of water molecules exhibiting enhanced orientational order, in the coordination sphere of large solutes. Finally, the source of the differences between Kauzmann's "hydrocarbon model" on protein denaturation and hydrophobic hydration is discussed, with relatively large amphiphilic hydrocarbons seemingly displaying a more similar behavior to some globular proteins than aliphatic hydrocarbons.
Preventing Chronic Disease

Introduction Participation in regular physical activity (PA) may help maintain bone health as people age. However, most American adults do not engage in the recommended minimum levels of PA, and there are racial/ethnic differences in PA participation. This study aimed to determine whether current physical activity is related to bone density in a racially/ethnically diverse sample after controlling for age, sex, body mass index, poverty–income ratio, tobacco use, vitamin D and calcium intake, and use of osteoporosis medications. Methods We obtained data on femoral bone mineral density for 2,819 adults aged 40 to 80 years who self-reported their race/ethnicity on the 2007–2008 National Health and Nutrition Examination Survey. Data on PA levels were obtained by self-report. We used linear regression models to examine the association between PA and bone density for each racial/ethnic group. Results A greater percentage of non-Hispanic blacks (60.9%) and Hispanics (53.3%) reported low levels of PA than nonHispanic whites (45.3%, P < .001). Non-Hispanic blacks (16.3%) and Hispanics (18.5%) had a lower prevalence of osteopenia than non-Hispanic whites (25.5%; P = .01) but were similar in the prevalence of normal and osteoporosis categories when compared with whites. There was a 0.031 g/cm difference in bone density between those in the high PA versus the low PA category (P = .003). This association remained (β = 0.027, P < .001) after adjusting for race/ethnicity, sex, body mass index, poverty–income ratio, tobacco use, and use of osteoporosis medications. Conclusion Despite lower levels of activity, blacks and Hispanics were not more likely to have osteoporosis, and high levels of activity were significantly associated with higher bone density even when controlling for race/ethnicity and confounders. The lack of consistency in bone density differences suggests that the cause of the differences maybe multifactorial. Introduction Osteoporosis is a chronic condition that is a major public health problem in the United States and around the world primarily because of the increased morbidity and mortality associated with osteoporotic fractures (1,2). Osteoporosis disproportionately affects the elderly, reducing their quality of life and contributing to declines in functioning, which in some instances can lead to the inability to remain in the community (2,3). In the past decade, large epidemiologic studies, using mostly non-Hispanic white samples, have contributed to understanding the risk factors of patients with osteoporosis and those who fracture (2,4). These studies suggest that men, women, and racial/ethnic minorities differ in terms of risk factors for osteoporosis and osteoporosis-related fractures (1,5). Furthermore, most research indicates 2 Page 1 of 10 Preventing Chronic Disease | Racial and Ethnic Differences in Physical Activity and Bon.
DMEM and FBS as thawing solutions for frozen semen of pigs can improve sperm motility and sow reproductive performance

The purpose of this experiment was to investigate the effects of Beltsville thawing solution BTS , Androhep, and Dulbecco? s modified Eagle medium + Fatal bovine serum D-F as diluents of frozen semen on sperm motility and sow reproductive performance. In experiment 1, boar semen was collected and diluted to 2.0 × 109/60 mL, 1.5 × 109/60 mL, and 1.5 × 109/40 mL with Androhep. The appropriate semen dose was determined by postcervical insemination. In experiment 2, boar semen was fumigated with liquid nitrogen and thawed semen was diluted to 1.5 × 109/40 mL with D-F, Androhep, and BTS, respectively. The effects of above diluents on sperm motility and sow reproductive performance were studied by postcervical insemination. The appropriate semen dose for postcervical insemination was 1.5 × 109/40 mL. After thawing of frozen semen, sperm motility of semen diluted with D-F was significantly higher than that of semen diluted with Androhep and BTS. There was no significant difference in pregnancy rates among sows via artificial insemination. The litter size of sows using D-F diluted semen was significantly higher than that of sows using Androhep and BTS diluted semen. In conclusion, D-F freezing diluent can improve sperm motility of frozen boar semen after thawing, prolong sperm survival time, and increase sow reproductive performance.
Comparing Automated Unit Testing Strategies

: Automated unit testing strategies that execute a large number of test cases are becoming more viable. In order to better understand the relationship be-tween these strategies, we deﬁne “explorative” unit testing strategies as those which choose unit tests by exploring a large search space with a simple structure, and we study three particular explorative strategies: bounded-exhaustive, randomized, and a combined strategy. In order to do this, we deﬁne canonical forms of unit tests and give precise deﬁnitions of the search spaces and strategies. We then show, by a combination of analysis and experimentation, that the bounded-exhaustive strategy is superior to randomized testing only when a small proportion of the search space of unit tests fails. We also show that we can arbitrarily and cost-effectively increase the failing proportion of the search space by simply increasing the number of method calls in the unit test.
An adaptive 3–D CFD solver for explosion modeling on large scales

An adaptive 3–D CFD solver for modeling detonations on large scales is presented. As a detonation itself is a small scale event, adaptive mesh refinement and coarsening is used to resolve all relevant scales. Results are compared with experimental data. Introduction Studies of gas cloud explosions in industrial environments increasingly rely on numerical simulations of the accident sequence. This field of study puts enourmous requirements on the numerical simulation methods for the following reasons: • The phenomena are inherently unsteady. • The geometrical configuration is often both very large and very complex. • The chemical source terms are highly nonlinear and require a very good spatial resolution. • In a gas explosion, chemistry and fluid flow are coupled by nonlinear effects, therefore a detailed modeling is needed here. • The total problem is a multi–scale problem in space and time, due to the fact that the geometrical scales vary from 10−3m for the flame itself to 10m for the size of the industrial environment. To cover most of these needs, the adaptive CFD code REACFLOW was developed at JRC-Ispra. In this extended abstract we describe briefly the governing equations and the adaptive methods for our 3–D version of the code. As a quantitative example a 3–D transient simulation of a detonation on large scale will be presented. Governing equations The governing fluid dynamics equations are the equations for conservation of mass, chemical species, momentum and energy. Due to the very short time scales of a detonation, diffusive processes do not have to be taken into account and only the Euler equations are solved. In weak form they can be written in the following compact notation (in a cartesian coordinate system)
Estimating natural illumination from a single outdoor scene Lalonde, Efros, Narasimhan - Analysis and Implementation

‘Illumination’ as an independent parameter, sets the context of an image as much as any other parameter would. As pointed out by [1], computer vision researchers have mostly been inclined to designing systems which are illumination invariant. The publication, “Estimating natural illumination from a single outdoor scene”, on the other hand has pointed out that one could use illumination as an important tool to better analyze images. We based our work on this publication and tried to estimate the illumination context of a natural scene from a single image. The paper uses the three most evident cues in a natural scene i.e. the sky, shadows on the ground and the varied intensities of the vertical surfaces to estimate the direction of light. They have pointed out that each of the three cues are not so strong themselves, but the combination of these weak cues give us a reliable estimate of the direction of the sun and the illumination context of the image. We have gone ahead and analyzed their work and tried to implement the idea on our own dataset. During the course of implementation, we have done a few things differently to see how the alternate approaches perform. To validate our work, we devised a simple experiment where we let people label the direction of the sun in the images in our dataset and compared the re-sults to what our algorithm generates. Not only did we get a good overview about the strengths and weaknesses of the approach taken by authors, we also realised that they were trying to solve a problem which is tough even for the human visual system.
Erysiphedeutziicola sp. nov. (Erysiphaceae, Ascomycota), a powdery mildew species found on Deutziaparviflora (Hydrangeaceae) with unusual appendages

Abstract A powdery mildew (Erysiphales) has recently been collected on leaves of an ornamental shrub Deutziaparviflora in Baihua Mountain, Beijing, China. Microscopic examination of the chasmothecia suggested a species belonging to Erysiphesect.Erysiphe, above all due to mycelioid chasmothecial appendages, although circinate apices of the appendages were rather in favour of Erysiphesect.Uncinula, which is a fairly rare combination of appendage characteristics in Erysiphe. Phylogenetic analyses of ITS and 28S rDNA sequences demonstrated that the two examined powdery mildew collections on D.parviflora clustered together as an independent lineage within Erysiphe with 100% bootstrap support, representing a species of its own, which is phylogenetically allied to, but clearly distinct from Erysiphedeutziae and, in addition, morphologically quite different from all known Erysiphe species on hosts belonging to the Hydrangeaceae. The new species on D.parviflora is described as Erysiphedeutziicola.
Growth Effect of Fiscal Policy in Dependent Natural Resources Countries: Case of a Monetary Union

This paper contributes to the understanding of the other neglected effects of fiscal policy by analyzing how it affects economic growth in developing countries over the period 1980? 2014.The empirical evidence is based on a Pooled Mean Group approach. With the panel of dependent natural resources countries that all are members of a Central Africa Economic and Monetary Community (CEMAC), the results show that fiscal policy measured as budget deficit has a positive and significant effect on growth in the short-run while it has a negative and significant effect on economic growth in the long run. The results of a short-run country effect analysis show the effectiveness of fiscal policy in all the countries of the union with an important effect in Equatorial Guinea and the less effect in Cameroon. There for, it would be important for the governments of these countries to diversify their economy, increase the share of manufacturing exports in their total exports and finally rigorously manage their public spending.
EFFECT OF THE NUMBER OF TAPPING BITS OF THE A5/1 STREAM CIPHER TOWARDS HARDWARE PERFORMANCE

: A5/1 stream cipher is a type of cryptographic algorithm which is widely used for encryption of the GSM communication. While numerous work on the modification of the conventional design of the A5/1 stream have been carried out, to the best of author’s knowledge, they are mainly tested in terms of the randomness (and hence security) level, whereas the practicality of the algorithm’s design in hardware is typically overlooked. Objective: In this paper, two modified designs proposed by the author are implemented into hardware and the resulting rate of power consumption is compared with that of the conventional design of the A5/1 stream cipher. Results: The results obtained shows that the rate of power consumption of the hardware is inversely proportional to that of the number of tapping bits used in the design. Conclusion: While the tapping bits are known to play a minor role when it comes to generating random binary sequence (and following it, the strength of the security of the design), it actually plays a positive role when it comes to increasing the efficiency of the performance of the hardware.
Characterization of PLA/Lignin Biocomposites for 3D Printing

A greater proportion of polymer-based three-dimensional (3D) printing materials are synthetic petroleum derivatives that are not biodegradable, contributing to environmental pollution and have potential adverse effects on human health. Polylactic acid (PLA) is currently the most widely used among the bio-based alternatives. This work explores alternative environmentally friendly bio-based polymers sourced from sustainable crop and forest biomass derivatives for 3D printing. Various blends of PLA/Organosolv lignin were extruded for fused filament fabrication (FFF) 3D printing process. The processing parameters and results of mechanical and thermal properties of fabricated test specimens of the biocomposite with up to 40wt% lignin concentration are presented. Results indicates that lignin, a low-cost waste product of pulping for the paper industry and bioethanol fuel production could serve as a key component of new biocomposite polymers for 3D printing applications.
Dynamics of protein-drug interactions inferred from structural ensembles and physics-based models

The conformational flexibility of target proteins is a major challenge in understanding and modeling protein-drug interactions. A fundamental issue, yet to be clarified, is whether the observed conformational changes are controlled by the protein, or induced by the inhibitor. While the concept of induced fit has been widely adopted for describing the structural changes that accompany ligand binding, there is growing evidence in support of the dominance of proteins' intrinsic dynamics, which has been evolutionarily optimized to accommodate its functional interactions. The wealth of structural data for target proteins in the presence of different ligands now permits us to make a critical assessment of the balance between these two effects in selecting the bound forms. We focused on three widely studied drug targets, HIV-1 reverse transcriptase, p38 MAP kinase, and cyclin-dependent kinase 2. A total of 292 structures determined for these enzymes in the presence of different inhibitors as well as unbound form permitted us to perform an extensive comparative analysis of the conformational space accessed upon ligand binding, and its relation to the intrinsic dynamics prior to ligand binding as predicted by elastic network model analysis. Further, we analyzed NMR ensembles of ubiquitin and calmodulin representing their microseconds range solution dynamics. Our results show that the ligand selects the conformer that best matches its structural and dynamic properties amongst the conformers intrinsically accessible to the protein in the unliganded form. The results suggest that simple but robust rules encoded in the protein structure play a dominant role in pre-defining the mechanisms of ligand binding, which may be advantageously exploited in designing inhibitors. We apply these lessons to the study of MAP kinase phosphatases (MKPs), which are therapeutically relevant but challenging signaling enzymes. Our study provides insights into the interactions and selectivity of MKP inhibitors and shows how an allosteric inhibition mechanism holds for a recently discovered inhibitor of MKP-3. We also provide evidence for the functional significance of the structure-encoded dynamics of rhodopsin and nicotinic acetylcholine receptor, members of two membrane proteins classes serving as targets for more than 40% of all current FDA approved drugs.
Generic Recognition for a Neglected Lineage of South American Pitvipers (Squamata: Viperidae: Crotalinae), with the Description of a New Species from the Colombian Chocó

Abstract The name Bothrops campbelli Freire-Lascano (1991) is currently applied to two distinct species. We restrict use of the name campbelli to the species that occurs on the western slopes of the Andes in Ecuador, and we describe the species that occurs in the Chocoan rainforest of western Colombia. Besides B. campbelli, the closest living relatives of the new species appear to be B. hyoprora and B. microphthalmus of the Atlantic slopes and lowlands of northern South America. Together these four species comprise a distinctive clade for which we propose the new generic name Bothrocophias.
Egalitarianism and the Corporate State in Latin America

Th e demise of the Pink Tide in Latin America has sparked much discussion as to whether this represents the end of left ist governmental experiments in the region and a return to what seems to be the status quo domination of right-wing conservative politics. Perhaps a more indicting implication of this debate is whether the Pink Tide represents an alternative to neoliberalism or whether it constitutes a particular typology of this system. Left -leaning scholars (Ackerman 2016; García Linera 2006; López Segrera 2016, among others) and activists counter this view by arguing that the Pink Tide has suffi ciently overturned traditional structures of domination and provided many disenfranchised groups with the concrete possibility of accessing political power. While we share the perception that the Pink Tide has indeed eff ected long-lasting transformations in Latin American political imaginaries and opened concrete lines for change, we are here concerned with the processes of structural transformation that underpin the formation of the Pink Tide and its more recent destabilization. As a response to the excesses of neoliberalism in the region, the Pink Tide has incorporated alternative egalitarian ideologies to political power. However, it has not been able to counteract the increasing corporatization of state structures taking place in Latin America – as in Europe and North America (as well as China and Russia but in diff erent confi gurations) – a process holistically aff ecting statehood, where neoliberalism is but one expression (as an ideology of the corporate state). A variety of responses have emerged in Latin America to what we identify as global processes of state transformation that indicate the emergence of
Polyamine metabolism and activation of lipid signalling pathways in Arabidopsis thaliana

Polyamine metabolism has emerged during the last 40 years as an important stress-related pathway and its accumulation is often a metabolic hallmark of enhanced plant stress tolerance. These small and versatile polycationic molecules are not only involved in stress responses, but also in many aspects of cellular biology and -physiology, affecting processes such as ion transport, protein- and lipid-kinase activity, transcription, protein synthesis, or stabilization of membrane- and nuclear components. Nonetheless, the molecular mechanism by which polyamines exert such a wide range of effects is still not well understood. To extend these studies, in this thesis we investigate the polyamine back-conversion pathway during salt stress in Arabidopsis thaliana using loss-of-function mutants of the AtPAO5 gene, the most-induced PAO member in salt conditions. In a different approach, we investigate the effect of polyamines on plasma membrane-associated phospholipid signalling, using an optimized 32Pi-labelling procedure that analyses phospholipid synthesis and turnover in vivo. In those studies, we demonstrate that polyamines trigger an increase of the lipid-signalling molecules phosphatidylinositol 4,5-bisphosphate and phosphatidic acid, in root cells of Arabidopsis seedlings. The detailed characterization of the phospholipid responses carried out in this thesis, provides novel and interesting tools to further unravel the role of polyamines in eukaryotic cell biology in general and in plant biology in particular.
The forage quality and the in vitro ruminal digestibility, gas production, organic acids, and some estimated digestion parameters of tomato herbage silage with molasses and barley

In this study, nutrient composition and use of silage after harvest of waste green parts herbage of tomato Licopersicon esculentum L. were researched as a wet forage source for ruminants. Three different silages of tomato herbage: without additive TS , with 5% sugar beet molasses TSm , or 5% crushed barley grain TSb were prepared. The forage quality and the in vitro ruminal digestibility, gas production, organic acids, and some estimated digestion parameters for different silages of tomato herbage were determined. Besides, the in vitro digestion values of using at 25%, 50%, 75%, and 100% rates instead of corn silage in the dairy cattle total mix ration TMR were researched. The lactic acid content of TSb silage was higher than those of the TS and TSm silages P 0.05 . Consequently, results have shown that tomato herbage should be ensiled with 5% molasses. However, it has been concluded that using tomato herbage silage with barley up to 75% or sugar beet molasses up to 100% instead of corn silage in dairy cattle ration did not have a negative effect in vitro.
The Osterix Reporter Mouse Identifies a Bone Marrow Skeletal Progenitor Cell Population

46 Introduction 47 Results 49 Chapter V: Defining the Osterix-Cherry+ Mesenchymal Progenitor within the Bone Marrow 63 Abstract: 63 63 Introduction: 65 Results: 67 LORE Cells Are Located Near the Endosteal Bone Surface and Are Associated with Vascular Sinusoids 67 Examination of Osterix Reporter Expression in Bone Marrow Stromal Cultures . 69 LORE Cells Retain Multipotent Skeletal Potential 71 Cell Surface Profiling and Gene Expression from LORE Cells Reveals Their Heterogeneity 73 Discussion: 78