bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Traveling Salesman Problem in the Natural Environment
Authors: Phillips Flip , O'Connell Thomas , Layton Oliver 
Published: July 2019

AbstractIs it possible for humans to navigate in the natural environment wherein the path taken between various destinations is &apos;optimal&apos; in some way? In the domain of optimization this challenge is traditionally framed as the &quot;Traveling Salesman Problem&quot; (TSP). What strategies and ecological considerations are plausible for human navigation? When given a two-dimensional map-like presentation of the destinations, participants solve this optimization exceptionally well (only 2-3% longer than optimum)^1, 2^. In the following experiments we investigate the effect of effort and its environmental affordance on navigation decisions when humans solve the TSP in the natural environment. Fifteen locations were marked on two outdoor landscapes with flat and varied terrains respectively. Performance in the flat-field condition was excellent (&8764;6% error) and was worse but still quite good in the variable-terrain condition (&8764;20% error), suggesting participants do not globally pre-plan routes but rather develop them on the fly. We suggest that perceived effort guides participant solutions due to the dynamic constraints of effortful locomotion and obstacle avoidance.
Evaluation of HIV infected Cells
Authors: Nallasamy Kumaresan 
Published: July 2019

AbstractIn this paper, Human Immunodeficiency Virus (HIV) infected cells is found out using a Simulink model. The Simulink solution is equivalent or very close to the exact solution of the problem. Accuracy of the Simulink solution to this problem is better than the existing numerical methods. The main advantage of Simulink model is that solution of any dynamicalproblem can be obtained by anybody without writing any codes. Anillustrative numerical example is presented for the proposed method.
Hierarchical nanomechanics of collagen microfibrils
Authors: Gautieri Alfonso , Vesentini Simone , Redaelli Alberto , Buehler Markus J. 
Published: July 2019

AbstractCollagen constitutes one third of the human proteome, providing mechanical stability, elasticity and strength to organisms and is thus the prime construction materials in biology. Collagen is also the dominating material in the extracellular matrix and its stiffness controls cell differentiation, growth and pathology. However, the origin of the unique mechanical properties of collagenous tissues, and in particular its stiffness, extensibility and nonlinear mechanical response remains unknown. By using x-ray diffraction data of a collagen fibril (Orgel et al., PNAS, 2006) here we present an experimentally validated model of the nanomechanics of a collagen microfibril that incorporates the full biochemical details of the amino acid sequence of constituting molecules. We demonstrate that mechanical testing of hydrated (wet) collagen microfibrils yields a Young’s modulus of ≈300 MPa at small and ≈1.2 GPa at larger deformation in excess of 10% strain, in excellent agreement with experimental data. Dehydrated (dry) collagen microfibrils show a significantly increased Young’s modulus of ≈1.8-2.25 GPa owing to a much tighter molecular packing, in agreement with experimental measurements. Our results demonstrate that the unique mechanical properties of collagen microfibrils arise due to their hierarchical structure, where key deformation mechanisms are straightening of twisted molecules at small strains, followed by axial stretching and eventual molecular uncoiling. These mechanisms explain the striking difference of the modulus of collagen fibrils compared with single molecules, which is found in the range of 4.8±2 GPa or ≈10-20 times greater. The atomistic model of collagen microfibril mechanics enables the bottom-up elucidation of structure-property relationships in a broader class of collagen materials (e.g. tendon, bone, cornea), including studies of genetic disease where the incorporation of biochemical details is essential.
The True Colours of Carbon
Authors: Thomas Sebastian , Hoegh-Guldberg Ove , Griffiths Andrew , Dargusch Paul , Bruno John 
Published: July 2019

AbstractCarbon offset projects in developing countries are one of the principal mechanisms designed to reduce greenhouse gas emissions and promote sustainable development yet have critical limitations in both areas. Here we present a framework for categorizing carbon offset projects according to four general approaches to the reduction of greenhouse gas emissions: (1) efficiency (&apos;Brown&apos;); innovation (&apos;Red&apos;), terrestrial sequestration (&apos;Green&apos;) or sequestration in aquatic environments (&apos;Blue&apos;). Analysis of the 6109 CDM projects currently in the CDM &quot;pipeline&quot; reveals that 99% are Brown or Red, and only 1% are Green or Blue, yet Green and Blue projects typically offer a far greater range of benefits for ecosystems and society. The analysis concludes that the designers of emissions trading schemes should endorse Green and Blue offset projects as preferred forms of emissions offsetting, and that firms using offsets for compliance purposes be required to declare in public reports the colours of their offset acquisitions. Such reform will help redirect demand in carbon markets toward blue and green offset projects, increasing the sustainability outcomes of carbon offset developments.
Self-organization of intrinsically disordered proteins with folded N-termini
Authors: Simister Philip , Schaper Fred , O'Reilly Nicola , McGowan Simon , Feller Stephan 
Published: July 2019

AbstractThousands of human proteins lack recognizable tertiary structure in most of their chains. Here we hypothesize that some use their structured N-terminal domains (SNTDs) to organise the remaining protein chain via intramolecular interactions, generating partially structured proteins. This model has several attractive features: as protein chains emerge, SNTDs form spontaneously and serve as nucleation points, creating more compact shapes. This reduces the risk of protein degradation or aggregation. Moreover, an interspersed pattern of SNTD-docked regions and free loops can coordinate assembly of sub-complexes in defined loop-sections and enables novel regulatory mechanisms, for example through posttranslational modifications of docked regions.
On the dimensionality of the Avogadro constant and the definition of the mole
Authors: Wheatley Nigel 
Published: July 2019

AbstractThere is a common misconception among educators, and even some metrologists, that the Avogadro constant _N_~A~ is (or should be) a pure number, and not a constant of dimension *N*^–1^ (where *N* is the dimension amount of substance). Amount of substance is measured, and has always been measured, as ratios of other physical quantities, and not in terms of a specified pure number of elementary entities. Hence the Avogadro constant has always been defined in terms of the unit of amount of substance, and not vice versa. The proposed redefinition of the mole in terms of a fixed value of the Avogadro constant would cause additional conceptual complexity for no metrological benefit.
Cholesterol Esterification During Differentiation by Hexamethylene Bisacetamide of Friend Virus-Induced Erythrokeukemia
Authors: Mulas Maria , Mandas Antonella , Abete Claudia , Dessi Sandra , Pani Mario , Manconi Rosa , Mocali Alessandra , Paoletti Francesco 
Published: July 2019

AbstractCholesterol is an essential constituent of all mammalian cell membranes, and its availability is therefore a prerequisite for cellular growth and other functions. Several lines of evidence are now indicating an association between alterations of cholesterol homeostasis and cell cycle progression in cancer cells. However, the role of cholesterol in cell differentiation is still largely unknown. To begin to address this issue, in this study we examined changes in cholesterol metabolism and in the mRNA levels of proteins involved in cholesterol import and esterification (multi-drug resistance, MDR-3) and acylCoA:cholesterol acyltransferase (ACAT) and cholesterol export (caveolin-1) in Friend virus-induced erythroleukemia cells (MELC), in the absence or in the presence of the chemical inducer of differentiation, hexamethylene bisacetamide (HMBA). In uninduced MELC, cholesterol synthesis, esterification and MDR-3 and ACAT mRNAs increased as cells progressed from resting to proliferating phase, while caveolin-1 decreased. These results provide evidence that cholesterol esterification “per se” may have a role in cell division. When MELC are treated with HMBA, the reduction of DNA synthesis caused by the inducer is accompanied by an extensive decrease of cholesterol esterification and of ACAT and MDR-3 mRNA levels and by a significant increase in caveolin-1 mRNA. On the other hand, detection of cytoplasmic neutral lipids by staining MELC with oil-ORO, a dye able to evidence CE but not FC, revealed that HMBA-treatment inhibits cholesterol ester accumulation in MELC to approximately the same extent as the ACAT inhibitor, SaH. These results, other than, to add new insights on the possible role of cholesterol metabolism during tumor growth, for the first time indicate a possible involvement of cholesterol esterification pathways in the regulating of differentiation of erythroleukemic cells.
Why do many animals move with a predominance of roughly forward directions?
Authors: Duffy Kevin 
Published: July 2019

AbstractAnimal movements can influence their ecology and demographics. Animal movements are often characterized by path structures with directional persistence. The extent to which directional persistence improves forage success is investigated in this paper using theoretical simulations. It is shown that a movement strategy with directional persistence enables simulated animals to find more forage as compared to a random movement strategy. Situations where resources are chosen with certainty (optimally) are even more successful. Choosing resource with certainty cannot result in directional persistence. However, in cases where animals choose with certainty adjacent cells with resource but continue in their existing direction if none of these have resources then results include directional persistence. It is posited here that this combined strategy is the most effective because if optimal foraging works it is optimally efficient but where foraging is sub-optimal, for a variety of reasons, directional persistence will benefit foraging.
Modeling Animal Movements in Response to Human Disturbances
Authors: Preisler Haiganoush , Ager Alan , Brillinger David , Wisdom Michael 
Published: July 2019

Abstract
Background/Question/Methods
The advent of GPS technology has made it possible to study human - wildlife interactions on large landscapes and quantify behavioral responses to recreation and other anthropogenic disturbances at increasingly fine scales. Of particular interest are the potential impacts on habitat use patterns, energetics, and cascading impacts on fecundity and other life history traits for key wildlife species that are increasingly exposed to human activities. However, the dynamics of free-ranging animal movements are complex, even without disturbances, and quantifying reactions to disturbance on heterogeneous landscapes is difficult. A modeling framework is required that can sort out diel and random movements that mask short and long-term behavioral response to disturbances.In this talk I will discuss how stochastic differential equations (SDE’s) are used to build potential function surfaces for describing movement patterns and responses to disturbances. I will demonstrate the methods using GPS data for free ranging elk within a 1450 ha study area on the Starkey Experimental Forest located in eastern Oregon. The telemetry data were collected as part of a long-term controlled experiment to understand the response of free ranging Rocky Mountain elk (Cervus elaphus) and deer (Odocoileus hemionus) to multiple anthropogenic disturbances including all terrain vehicles, hikers, mountain bikers and equestrians. This work includes the development of statistical procedures to estimate the simultaneous effects of two or more entities (combinations of animals and disturbance agents) on the potential surfaces, to understand the effects of multiple interacting disturbances on observed patterns of movement.2)

Results/Conclusions
We parameterized stochastic differential equations to quantify effects of topography; distance to roads; distance to disturbance, and random movements on elk locations. The GPS technology provided evidence that: 1) elk appear to know the location of roads and the routing of traffic on roads through the forest; 2) hikers and equestrians seem to generate a larger movement response compared to mountain bikers and ATV riders; and, 3) The threshold response distance appears to be well beyond those previously reported in studies that relied on visual methods.The study demonstrated the utility of SDE’s and the motivating concept of potential functions to model animal movements. These methods have also been applied by the authors to study movement patterns in yellow legged frogs (Rana sierrae), elephant seals (Mirounga angustirostris), Monk seals (Monachus schauinslandi) and whale sharks (Rhincodon typus ).
Ultrasonic frogs show extraordinary sex differences in auditory frequency sensitivity
Authors: Shen Jun-Xian , Xu Zhi-Min , Yu Zu-Lin , Wang Shuai , Zheng De-Zhi 
Published: July 2019

AbstractAcoustic communication plays an important role in the reproductive behavior of anurans. Males of concave-eared torrent frog (_Odorrana tormota_) have ultrasonic communication capacity 1, 2, but it is unknown whether females communicate with ultrasound. Here we show that O. tormota exhibits great sex differences in the auditory frequency sensitivity. Acoustic playback experiments demonstrated that the male's advertisement calls evoke gravid females' positive phonotaxis and vocal responses, whereas ultrasonic components of the male's calls (frequencies above 20 kHz) do not elicit female phonotaxis or vocalization. The behavioral study was complemented by electrophysiological recordings from the auditory midbrain and by laser Doppler vibrometer measurements of the tympanic membrane's response to acoustic stimuli. These measurements revealed that females have an upper frequency limit up to 16 kHz (threshold 107 dB SPL) and no ultrasound sensitivity, unlike males which have an upper frequency limit of up to 35 kHz (87 dB SPL). Single units in the female auditory midbrain have the best excitatory frequencies (BEFs) peaked around 5 kHz, corresponding to the fundamental frequency (F0) of male's most calls, whereas the male auditory midbrain units have BEFs mostly above 8 kHz, largely consistent with the F0 of female courtship calls. Females have a frequency sensitive bandwidth (10 dB above threshold) ranged from 2 to 6 kHz, narrower than that males have (5-20 kHz). The velocity amplitude of the tympanic membranes peaked around 5 kHz in females, whereas 7 kHz in males. The results suggest that the frog species O. tormota is an example of a vertebrate, which demonstrates well phonotaxis and extraordinary sex differences in hearing.
Where is the ‘Jennifer Aniston neuron’?
Authors: Aur Dorian , Steinmetz Peter 
Published: July 2019

AbstractIt is generally believed that spike timing features (firing rate, ISI) are the main characteristics that can be related to neural code. Contrary to this common belief, spike directivity, a new measure that quantifies transient charge density dynamics within action potentials (APs) provides better results in discriminating different categories of visual object recognition. Specifically, intracranial recordings from medial temporal lobe (MTL) of epileptic patients have been analyzed using firing rate, interspike intervals and spike directivity. A comparative statistical analysis of the same spikes from four selected neurons shows that electrical micro-mapped features in neurons display higher separability to input images compared to spike timing features. If the observation vector include data from all 4 neurons then the comparative analysis shows a highly significant separation between categories for spike directivity (p=0.0023) and does not display separability for ISI (p=0.3768) and firing rate (p=0.5492). The presence of electrical micro-maps within APs suggests the existence of an intrinsic “neural code" where information regarding input images is electrically written/coded and read/decoded during AP propagation in the neuron. The occurrence of electrical micro-maps within APs reflects information communication and computation in analyzed neuron within a millisecond-level time domain of AP occurrence. This existence of a “lower level” of coding where information is processed within neurons raises questions regarding the richness and reliability of models that constrain neural code to spike timing features. Additionally, this phenomenon that occurs within APs may provide a step forward in understanding the fundamental gap between molecular description, information processing and neuronal function. Importantly, this paper confirms a new paradigm regarding neural code where information processing, computation and memory formation in the brain can be explained in terms of dynamics and interaction of electric charges.
A logistic regression model for microalbuminuria prediction in overweight male population
Authors: Chen BaoDe , Xu WeiYi , Yu Chen , Ni ZhenYun , Li XueFen , Cui DaWei 
Published: July 2019

Abstract
Background:
Obesity promotes progression to microalbuminuria and increases the risk of chronic kidney disease. Current protocols of screening microalbuminuria are not recommended for the overweight or obese.Design and Methods: A cross-sectional study was conducted. The relationship between metabolic risk factors and microalbuminuria was investigated. A regression model based on metabolic risk factors was developed and evaluated for predicting microalbuminuria in the overweight or obese.

Results:
The prevalence of MA reached up to 17.6% in Chinese overweight men. Obesity, hypertension, hyperglycemia and hyperuricemia were the important risk factors for microalbuminuria in the overweight. The area under ROC curves of the regression model based on the risk factors was 0.82 in predicting microalbuminuria, meanwhile, a decision threshold of 0.2 was found for predicting microalbuminuria with a sensitivity of 67.4% and specificity of 79.0%, and a global predictive value of 75.7%. A decision threshold of 0.1 was chosen for screening microalbuminuria with a sensitivity of 90.0% and specificity of 56.5%, and a global predictive value of 61.7%.

Conclusions:
The prediction model was an effective tool for screening microalbuminuria by using routine data among overweight populations.
Origin of biological information: Inherent occurrence of intron-rich split genes, coding for complex extant proteins, within pre-biotic random genetic sequences
Authors: Senapathy Periannan , Kumar Brajendra , Singh Chandan , Senapathy Sudar , Balan Bipin , Kuppuswami Raj 
Published: July 2019

AbstractThe origin of biological information is an unexplained phenomenon. Prior research in resolving the origin of proteins, based on the assumption that the first genes were contiguous prokaryotic sequences has not succeeded. Rather, it has been established that contiguous protein-coding genes do not exist in practically any amount of random genetic sequences. We found that complex eukaryotic proteins could be inherently encoded in split genes that could exist by chance within mere micrograms to milligrams of random DNA. Using protein amino acid sequence variability, codon degeneracy, and stringent exon-length restriction, we demonstrate that split genes for proteins of extant eukaryotes occur extensively in random genetic sequences. The results provide evidence that an abundance of split genes encoding advanced proteins in a small amount of prebiotic genetic material could have ignited the evolution of the eukaryotic genome.
Methanogen consortium metabolism characteristic analysis of Illinois basin by real time monitor method
Authors: Xiao Dong , Wang Enyuan 
Published: July 2019

AbstractMicrobially Enhance Coalbed Methane technology is used to improve methane content in coalbeds. The methanogen consortium metabolism process is the basic avenue for MECoM to yield methane with some organic compounds in coal. Detailed information about the metabolism process is needed in studying the microbial consortium mechanism. Traditional gas analysis is limited by gas source and test complexity. The real time monitor with Infrared gas sensor breaks the gas analysis limitation. It shows much more detailed information than the traditional analysis method including information about microbial growth factor changes, reaction speeds for environmental changes, the detailed relationship between CH4 and CO2, methane yield and the consumption factor by real time. With these factors, MECoM can be much better evaluated and controlled. Experiments show that inhibitory and incentive effects will influence the whole organic material conversion to methane period. Not until a microbial community achieves a balanced condition, can methane generation reach a stable condition.
Co-transformation of Oil Palm Using Agrobacterium-Mediated Transformation
Authors: Le Vu 
Published: July 2019

AbstractAgrobacterium-mediated transformation is being used as an alternative method for improving the conventional breeding. In this study, immature embryos (IEs) of oil palm are chosen as explants for transformation. &x03B2;-glucuronidase (gus) and green fluorescence protein (GFP) were harbored by the two plasmids pCAMBIA 1304 and pCAMBIA 1302 respectively. The results were obtained at least four days after transformation. The IEs placing in the N6O medium for 7 days were then co-cultivated with A.tumefaciens suspension within 30 mins and then incubated in the dark for 1 day. In single transformation, GUS assay revealed that about 64% transient transformation frequency was obtained for IEs two weeks after co-cultivation, GFP activity was recorded as 41.67% transformation frequency for IEs 4 days after co-cultivation. In co-transformation, the transformation frequency was lower than single transformation and there was no GFP activity recorded in co-transformation.
Grb2 binds to PTEN and regulates its nuclear translocation to maintain the genomic stability in DNA damage response
Authors: Hou Bolin , Xu Shanshan , Xu Yang , Gao Quan , Zhang Caining , Liu Ling , Yang Huaiyi , Jiang Xuejun , Che Yongsheng 
Published: July 2019

AbstractGrowth factor receptor bound protein 2 (Grb2) is an adaptor protein critical for signal transduction and endocytosis, but its role in DNA damage response (DDR) remains unknown. Here, we report that either knockdown of Grb2 or overexpression of the mutated Grb2 promotes micronuclei formation in response to oxidative stress. Furthermore, Grb2 was demonstrated to interact with phosphatase and tensin homologue (PTEN; a tumor suppressor essential for nuclear stability), and the loss of Grb2 reduced the nuclear-localized PTEN, which was further decreased upon stimulation with hydrogen peroxide (H2O2). Overexpression of the T398A-mutated, nuclear-localized PTEN reduced micronuclei frequency in the cells deficient of functional Grb2 via rescuing the H2O2-dependent expression of Rad51, a protein essential for the homologous recombination (HR) repair process. Moreover, depletion of Grb2 markedly decreased the expression of Rad51 and its interaction with PTEN. Notably, Rad51 showed a preference to immunoprecipation with the T398A-PTEN mutant, and silencing of Rad51 alone accumulated micronuclei concurring with decreased expression of both Grb2 and PTEN. Our findings indicate that Grb2 interacts with PTEN and Rad51 to regulate genomic stability in DDR by mediating the nuclear translocation of PTEN to affect the expression of Rad51.