bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome-wide analysis to predict protein sequence variations that change phosphorylation sites or their corresponding kinases
Authors: Ryu Gil-Mi , Song Pamela , Kim Kyu-Won , Oh Kyung-Soo , Kim Jong Hun 
Published: July 2019

AbstractWe define phosphovariants as genetic variations that change phosphorylation sites or their interacting kinases. Considering the essential role of phosphorylation in protein functions, it is highly likely that phosphovariants change protein functions and may constitute a proportion of the mechanisms by which genetic variations cause individual differences or diseases. We categorized phosphovariants into three subtypes and developed a system that predicts them. Our method can be used to screen important polymorphisms and help to identify the mechanisms of genetic diseases.
Fossil evidence for the origin of spider spinnerets
Authors: Selden Paul , Shear William 
Published: July 2019

AbstractSilk production from opisthosomal glands is a defining characteristic of spiders (Araneae). Silk emerges from spigots (modified setae) borne on spinnerets (modified appendages). Spigots from Attercopus fimbriunguis (Shear, Selden & Rolfe, 1987^1^), from Middle Devonian (386 Ma) strata of Gilboa, New York were described in 1989^2^ as evidence for the oldest spider and the first use of silk by animals. Slightly younger (374 Ma) material from South Mountain, New York, conspecific with A. fimbriunguis, includes spigots and other evidence which elucidate the evolution of early Araneae and the origin of spider silk. No known Attercopus spigots, including the original specimen^2^, occur on true spinnerets but are arranged along the edges of plates. Spinnerets originated from biramous appendages of opisthosomal somites 4 and 5; while present in Limulus, no other arachnids have opisthosomal appendage homologues on these segments. The spigot arrangement in Attercopus shows a primitive state prior to the re-expression of the dormant genetic mechanism which gave rise to spinnerets in later spiders. The inability of Attercopus precisely to control silk weaving suggests its original use as a wrapping, lining or homing material.
How do you choose your literature search tool(s)?
Authors: Acharya Kshitish , Kasliwal Greta , Haridas Haritha 
Published: July 2019

AbstractWith increasing number of bio-literature search engines, scientists and health professionals either make a subjective choice of tool(s) or face a challenge of analyzing multiple features of a plethora of bibliographic software. There is an urgent need for a thorough comparative analysis of the available literature scanning tools, from the user’s perspective. We report results of the first time semi-quantitative comparison of 21 search programs, which can search published (partial or full text) documents in life science areas. The observations can assist life science researchers and medical professionals to make an informed selection among the programs, depending on their search objectives. Some of the important findings are: 1. Most of the hits obtained from Scopus, ReleMed, EBImed, CiteXplore, and HighWire Press were usually relevant (i.e., these tools showed a better precision than other tools). 2. But a very high number of relevant citations were retrieved by HighWire Press, Google Scholar, CiteXplore and Pubmed Central (they had better recall). 3. HWP and CiteXplore seemed to have a good balance of precision and recall efficiencies. 4. PubMed Central, PubMed and Scopus provided the most useful query systems. 5. GoPubMed, BioAsk, EBIMed, ClusterMed could be more useful among the tools that can automatically process the retrieved citations for further scanning of bio-entities such as proteins, diseases, tissues, molecular interactions etc). The authors suggest the use of PubMed, Scopus, Google Scholar and HighWire Press - for better coverage, and GoPubMed - to view the hits categorized based on the MeSH and gene ontology terms.
Threshold Decline in Mesoamerican Coral Growth and Resiliency
Authors: Carilli Jessica , Norris Richard 
Published: July 2019

AbstractCaribbean coral reefs have been massively altered in recent decades due to human impacts, resulting in a dramatic reduction of live coral cover but quantitative data before the 1970s have not been available to assess how these changes came about1,2,3. We produced master chronologies of growth rates in massive Montastrea faveolata corals from the Mesoamerican reef tract that provide a method for extending records of coral health further back into the past. Our records reveal a unique reduction in growth rate associated with the 1998 coral bleaching event that has no parallel in the past 75 to 150 years. Of 92 cores collected from live coral heads in 2006-2007, 94% have severely reduced growth rates and 14% exhibit partial mortality scars in 1998-1999 whereas only 3 stress bands are found in single cores prior to 1998, and none of these cores exhibited earlier partial mortality. Some corals returned to pre-1998 extension rates by 2001, although corals in areas affected by sediment-laden runoff or high human population density still had not fully recovered by the time of sample collection eight years later. Previous episodic stresses like hurricane strikes and a warming event in 1983 more severe than 1998 had little to no effect on M. faveolata growth rates. The 1998 event apparently surpassed a threshold in coral tolerance precipitating a catastrophic shutdown in growth that had lasting effects throughout the Mesoamerican reef system but was particularly prolonged in areas exposed to other stressors. These findings suggest that projected increases in global temperatures over the next century are likely to result in drastic reductions in growth rather than a gradual decline in coral health, but that corals with fewer local stresses will be better able to survive bleaching events, underscoring the need for local conservation measures.
Binge and Emotional Eating in obese subjects seeking weight loss treatment
Authors: Ricca Valdo , Castellini Giovanni , Lo Sauro Carolina , Ravaldi Claudia , Lapi Francesco , Mannucci Edoardo , Rotella Carlo Maria , Faravelli Carlo 
Published: July 2019

Abstract
Objective:
Binge Eating Disorder (BED) is highly prevalent among individuals seeking weight loss treatment. Considering the possible trigger factors for BED, different studies focused on the role of emotional eating. The present study compared threshold, subthreshold BED, and subjects without BED in a population of overweight/obese individuals seeking weight loss treatment, considering the anamnesis, the eating disorder specific and general psychopathology, the organic and psychiatric comorbidity, the emotional eating as a trigger factor for binge eating, and the quality of life. Design: cross-sectional survey.

Subjects:
Four hundred thirty eight overweight subjects seeking weight loss treatment have been enrolled in the study. Measurements: Subjects have been evaluated by means of a clinical interview (SCID I) and different self-reported questionnaires (Eating Disorder Examination Questionnaire, Binge Eating Scale, Beck Depression Inventory, Spielberg&apos;s State-Trait Anxiety Inventory, Symptom Checklist 90, Emotional Eating Scale, and Obesity Related Well-Being questionnaire).

Results:
One hundred and five subjects (24% of the sample) fulfilled the DSM-IV criteria of lifetime BED, 146 (33.3%) fulfilled the criteria of lifetime subthreshold BED, and 187 (42.7%) subjects were diagnosed overweight non-BED. No correlations between the binges frequencies and the overweight levels were found. All the three groups showed high psychiatric comorbidities, and the three groups significantly differed in terms of emotional eating, which was positively correlated to the binge eating frequencies.

Conclusions:
Threshold and subthreshold BED deserve a careful psychopathological investigation and emotional eating seems to play a key role as trigger factor for binge eating. Obesity is associated with a high psychiatric comorbidity and a low quality of life, independently from the specific and general eating disorder psychopathology.
Technological Solutions for Energy Security and Sustainability
Authors: Werbos Paul 
Published: July 2019

AbstractThis paper addresses the question: how can we minimize the expected time between now and the time when we achieve three measures of sustainability and security together — independence from oil in cars and trucks, very deep reductions in greenhouse gas emissions and deep reductions in natural gas for electricity? Specific new technologies and metrics for progress are discussed, in context, linked to new information from IEEE, NSF, the State of the Future project and other sources.
Decoding the Design Principles of Amino Acids and the Chemical Logic of Protein Sequences
Authors: Jayaram B. 
Published: July 2019

AbstractThat only 20 amino acids occur naturally accounting for the structural and functional diversity of proteins remains a mystery. We show here that this is a consequence of the action of a symmetry group, identify the presence of hydrogen bond donor groups, presence of sp3 hybridized [gamma] carbons, absence of [delta] carbons and linearity as properties central to side chain design and quantify the chemical logic of protein sequences.
PocketMatch: A new algorithm to compare binding sites in protein structures
Authors: Kalidas Yeturu , Chandra Nagasuma 
Published: July 2019

Abstract
Background:
Recognizing similarities and deriving relationships among protein molecules is a fundamentalrequirement in present-day biology. Similarities can be present at various levels which can be detected through comparison of protein sequences or their structural folds. In some cases similarities obscure at these levels could be present merely in the substructures at their binding sites. Inferring functional similarities between protein molecules by comparing their binding sites is still largely exploratory and not as yet a routine protocol. One ofthe main reasons for this is the limitation in the choice of appropriate analytical tools that can compare binding sites with high sensitivity. To benefit from the enormous amount of structural data that is being rapidly accumulated, it is essential to have high throughput tools that enable large scale binding site comparison.

Results:
Here we present a new algorithm PocketMatch for comparison of binding sites in a frame invariantmanner. Each binding site is represented by 90 lists of sorted distances capturing shape and chemical nature of the site. The sorted arrays are then aligned using an incremental alignment method and scored to obtain PMScores for pairs of sites. A comprehensive sensitivity analysis and an extensive validation of the algorithm have been carried out. Perturbation studies where the geometry of a given site was retained but the residue types were changed randomly, indicated that chance similarities were virtually non-existent. Our analysis also demonstrates that shape information alone is insufficient to discriminate between diverse binding sites, unlesscombined with chemical nature of amino acids.

Conclusions:
A new algorithm has been developed to compare binding sites in accurate, efficient andhigh-throughput manner. Though the representation used is conceptually simplistic, we demonstrate that alongwith the new alignment strategy used, it is sufficient to enable binding comparison with high sensitivity. Novel methodology has also been presented for validating the algorithm for accuracy and sensitivity with respect to geometry and chemical nature of the site. The method is also fast and takes about 1/250th second for one comparison on a single processor. A parallel version on BlueGene has also been implemented.
Pegs and Ropes: Geometry at Stonehenge
Authors: Johnson Anthony , Pimpinelli Alberto 
Published: July 2019

AbstractA recent computer-aided-design investigation of the Neolithic 56 Aubrey Hole circuit at Stonehenge has led to the discovery of an astonishingly simple geometrical construction for drawing an approximately regular 56-sided polygon, feasible with a compass and straightedge. In the present work, we prove analytically that the aforementioned construction yields as a byproduct, an extremely accurate method for approximating a regular heptagon, and we quantify the accuracy that prehistoric surveyors may have ideally attained using simple pegs and ropes. We compare this method with previous approximations, and argue that it is likely to be at the same time the simplest and most accurate. Implications of our findings are discussed.
Courtship plasticity reveals the evolution of dialects in allopatric fish populations
Authors: Gonzalez Zuarth Cesar , Vallarino Adriana , Macias Garcia Constantino 
Published: July 2019

AbstractTraditionally, reproductive isolation between disjoint populations has been thought to emerge as a result of the accumulation of different mutations, genetic drift, or through the effects of natural and sexual selection^1^. Alternatively, the ability of an organism to express different phenotypes depending on the environment (i.e. phenotypic plasticity) could produce reproductive isolation^2,3^. Sexually selected traits are expected to be phenotypically plastic and can result in modifications of the species recognition system and thus originate new species^4^. Here we show that the population-characteristic male courtship behaviour of a fish (Girardinichthys multiradiatus) is modified in the presence of females from other populations, that this is due to the males responding to subtle cues from females, and that they fail to emulate the female&apos;s population-characteristic behaviour. We conclude that plasticity has led to the creation of local dialects in the courtship pattern that hampers communication between heterogametic individuals and promotes pre-mating isolation.
Successful use of axonal transport for drug delivery by synthetic molecular vehicles
Authors: Filler Aaron , Whiteside Garth , Bacon Mark , Frederickson Martyn , Howe Franklyn , Rabinowitz Miri , Sokoloff Alan , Deacon Terrence , Abell Chris , Munglani Raj , Griffiths John , Bell B. Anthony , Lever Andrew 
Published: July 2019

AbstractWe report the use of axonal transport to achieve intraneural drug delivery. We constructed a novel tripartite complex of an axonal transport facilitator conjugated to a linker molecule bearing up to a hundred reversibly attached drug molecules. The complex efficiently enters nerve terminals after intramuscular or intradermal administration and travels within axonal processes to neuron cell bodies. The tripartite agent provided 100-fold amplification of saturable neural uptake events, delivering multiple drug molecules per complex. in vivo, analgesic drug delivery to systemic and to non-targeted neural tissues was greatly reduced compared to existing routes of administration, thus exemplifying the possibility of specific nerve root targeting and effectively increasing the potency of the candidate drug gabapentin 300-fold relative to oral administration.
Exaptation and emergence as mechanisms to cross fitness valleys during evolution: an example using simulated homing behaviour
Authors: Stafford Richard 
Published: July 2019

AbstractEvolution is often considered a gradual hill climbing process, slowly increasing the fitness of organisms. I investigate the evolution of homing behaviour in simulated intertidal limpets. In order to evolve path integration as a homing mechanism, a temporary reduction in an organism’s fitness is required – since high developmental costs occur before a successful homing strategy evolves. Simple hill-climbing algorithms, therefore, only rarely result in the evolution of a functional homing behaviour. The inclusion of a second behaviour (trail-following) greatly increases the frequency of success of evolution of a path integration strategy. Initially an emergent homing behaviour is formed combining path integration with trail following. This also demonstrates evolution through exaptation, since the original role of trail following is likely to be unrelated to homing. Analysis of the fitness landscapes of homing in the presence of trail-following behaviour shows a high variability of fitness, which results in the formation of ‘stepping-stones’ of high fitness across fitness valleys. By using these stepping-stones, simple hill-climbing algorithms can reach the global maximum fitness value.
Stress responsive miR-23a attenuates skeletal muscle atrophy by targeting MAFbx /atrogin-1
Authors: Wada Shogo , Kato Yoshio , Okutsu Mitsuharu , Miyaki Shigeru , Suzuki Katsuhiko , Yan Zhen , Asahara Hiroshi , Ushida Takashi , Akimoto Takayuki 
Published: July 2019

AbstractMuscle atrophy occurs in many pathological states and results primarily from accelerated protein degradation by the ubiquitin-proteasome pathway. We used dexamethasone to induce muscle wasting and investigated the role of a microRNA (miRNA) in the control of muscle-specific E3 ubiquitin ligase MAFbx/atrogin-1. Here we show that miR-23a suppresses MAFbx/atrogin-1 translation by binding to 3'UTR of the mRNA. Furthermore, ectopic expression of miR-23a is sufficient to protect myocytes from atrophy in vitro and in vivo in response to dexamethasone treatment, and heat stress-induced miR-23a protects muscle from dexamethasone-induced muscle atrophy. Our surprising discovery of the physiological role of miR-23a in preventing the atrophy program should lay the basis not only for further understanding of the mechanisms of muscle wasting in diverse diseases, but also for developing novel therapies for these debilitating conditions.
Building Block and Building Rule: Dual Descriptor Method for Biological Sequence Analysis
Authors: Ma Bin-Guang 
Published: July 2019

AbstractThe emergence of “Systems Biology” in recent years highlights the systematic viewpoint of bio-system modeling. Building on such a background, Dual Descriptor Method, a generic methodology for biological sequence analysis is proposed. From a systematic perspective, Dual Descriptor is defined as a two element set of Composition Weight Map and Position Weight Function which aim at reflecting the composition and permutation information of a sequence. An alternate training algorithm is provided to get an optimum description of the building patterns of the sequences. In this paper, dual descriptor method has been applied to the analysis of two typical problems of molecular biology: gene identification and the prediction of protein function. Satisfactory and insightful results are achieved. Owing to the generality of this methodology, dual descriptor method has wide application perspective for many problems of pattern recognition, especially those involved in “Systems Biology”.
Logic motif of combinatorial control in transcriptional networks
Authors: Wu Xuebing , Sun Zhirong , Jiang Rui 
Published: July 2019

AbstractCombinatorial control is prevalent in transcriptional regulatory networks. However, whether there are specific logic patterns over- or under-represented in real networks remains uninvestigated. Using a theoretic model and in-silico simulations, we systematically study how the relative abundance of distinct regulatory logic patterns influences the network’s global dynamics. We find that global dynamic characteristics are sensitive to several specific logic patterns regardless of the detailed network topology. We show it is possible to infer logic motifs based on the sensitivity profile and the biological interpretations of these global characteristics.
Testing a new intervention to enhance road safety
Authors: Spiegel Rainer , Kalla Roger , Spiegel Frank , Strupp Michael 
Published: July 2019

AbstractBy 2020, it is estimated that road accidents will have moved from ninth to third in the worldwide ranking of burden of disease, as assessed in the disability adjusted life years (DALY)^1,2^. Therefore, it is vital to find effective methods to enhance road safety. Speed limits and traffic calming have the potential to reduce injuries due to road accidents^3,4^. Many drivers, however, do not adhere to speed limits^1-7^. Several studies have shown that adherence to speed limits can be explained by the theory of planned behaviour ^5-7^ and that it is possible to focus on drivers' intentions via self-report questionnaires. It is often difficult, however, to reach the majority of drivers on accident-prone locations with self-report questionnaires. This paper demonstrates an intervention that can be interpreted in the light of two of the theory's key variables^8^. It also has the potential to reach a large number of drivers on such locations. It is a speed-displaying device mounted next to the road (especially in villages). It tells drivers their actual speed (which is publicly visible). The measurement takes place continuously, giving the driver the chance to adjust speed and see the new speed shortly thereafter. The results show that the feedback about the current speed is associated with a significant speed reduction relative to a Control condition.
Low Cardiorespiratory Fitness is an Independent Predictor of Metabolic Syndrome in Young Korean Adults
Authors: Kang Hyun-Sik , Park Soo-Hyun , Kim Shinuk 
Published: July 2019

Abstract
Objective:
To investigate the relationship between cardio/respiratory fitness (CRF) and metabolic syndrome (MS) in young Korean men. Design: In a cross-sectional study, we examined 909 young Korean men (mean&177;SD age, 24.0&177;2 years) who were healthy and not taking any medications affecting blood pressure, glucose, or lipids concentrations. Body fatness, resting blood pressures, and fasting blood levels of lipids, glucose, and insulin were measured with our standardized laboratory protocols. CRF was quantified as the maximum volume of minute oxygen consumption measured during a graded treadmill test. Metabolic syndrome was defined with the National Cholesterol Education Program Adult Treatment Panel III criteria and a modified cut-off value of waist circumference from the Asia-Pacific Perspective: Redefining Obesity and its Treatment.

Results:
Group analyses showed significant and inverse dose-response trends between the metabolic syndrome markers and CRF levels such that men with high and moderate CRF levels had more favorable profiles in body fatness, resting blood pressures, mean values in fasting lipids, glucose, and insulin, and homeostasis model of assessment-insulin resistance than men with low CRF level. After adjusting for several potential confounders such as age, smoking, and body fatness variables, the low and moderate CRF groups had odds of 4.64 (95% CI, 2.00 to 10.79) and 2.57 (95% CI, 1.04 to 6.34) for having metabolic syndrome than the high CRF group. Conclusion: These findings suggest that low CRF is a significant and independent risk factor for metabolic syndrome in young Korean men.