bluuebunny/crossref_metadata_2025_split huggingface dataset:
Increasing Insect Reactions in Alaska: Is this Related to Changing Climate?
Authors: Demain Jeffrey , Gessner Bradford , McLaughlin Joseph , Sikes Derek , Foote Timothy 
Published: July 2019

AbstractDuring the summer of 2006, Fairbanks Alaska experienced its first two known cases of fatal anaphylaxis as a result of Hymenoptera stings, presumably from yellowjackets. An increase in insect bites and stings has been observed throughout the state.Has there been an increased incidence of medical visits due to insect bites and stings in Alaska in recent years? We conducted a retrospective review of three independent patient databases in Alaska to identify trends of patients seeking medical care for adverse reactions following insect bites and stings. For each database, an insect bite or sting episode warranting medical care was defined as a claim for the Clinical Modification of the International Classification of Diseases, Ninth Revision (ICD-9-CM), codes E905.3 (venomous insect; Hymenoptera); E906.4 (bite; non-venomous arthropod), and 989.5 (toxic effect; venom). Increases in bite and sting events in each region were compared to temperature changes in the same region. Each database revealed a statistically significant trend in patients seeking care for reactions to insect bites and stings. Fairbanks Memorial Hospital Emergency Department reported a four-fold increase in patients in 2006 compared to previous years (1992-2005). The Allergy Asthma and Immunology Center of Alaska reported a three-fold increase in patients from 1999 - 2002 to 2003- 2007. A retrospective review of the Alaska Medicaid database between 1999 and 2006 showed increases in billings for insect bites and stings among all regions, with the largest percentage increases occurring in the most northern areas. Alaska has experienced an increase in insect bites and stings, most dramatically indicated by two anaphylaxis deaths due to Hymenoptera stings. Statistically significant increases in patients seeking medical care for insect bite and sting related events are observed throughout the state, with 5 of the 6 regions experiencing at least a 6 degree Fahrenheit increase in winter temperature since 1950.
Searching the World-Wide-Web using nucleotide and peptide sequences
Authors: Ganesan Natarajan , Bennett Nicholas , Kalyanasundaram Bala , Velauthapillai Mahe , Squier Richard 
Published: July 2019

Abstract
*Background:*
No approaches have yet been developed to allow instant searching of the World-Wide-Web by just entering a string of sequence data. Though general search engines can be tuned to accept ‘processed’ queries, the burden of preparing such ‘search strings’ simply defeats the purpose of quickly locating highly relevant information. Unlike ‘sequence similarity’ searches that employ dedicated algorithms (like BLAST) to compare an input sequence from defined databases, a direct ‘sequence based’ search simply locates quick and relevant information about a blunt piece of nucleotide or peptide sequence. This approach is particularly invaluable to all biomedical researchers who would often like to enter a sequence and quickly locate any pertinent information before proceeding to carry out detailed sequence alignment.

*Results:*
Here, we describe the theory and implementation of a web-based front-end for a search engine, like Google, which accepts sequence fragments and interactively retrieves a collection of highly relevant links and documents, in real-time. e.g. flat files like patent records, privately hosted sequence documents and regular databases.

*Conclusions:*
The importance of this simple yet highly relevant tool will be evident when with a little bit of tweaking, the tool can be engineered to carry out searches on all kinds of hosted documents in the World-Wide-Web.*Availability:* Instaseq is free web based service that can be accessed by visiting the following hyperlink on the WWWhttp://instaseq.georgetown.edu
Microbial ecosystem constructed in water for successful organic hydroponics
Authors: Shinohara Makoto , Ohmori Hiromi , Uehara Yoichi 
Published: July 2019

AbstractConventional hydroponics systems generally use only chemical fertilisers, not organic ones, since there are no microbial ecosystems present in such systems to mineralise organic compounds to inorganic nutrients. Addition of organic compounds to the hydroponic solution generally has phytotoxic effects and causes poor plant growth. We developed a novel hydroponic culture method using organic fertiliser. A microbial ecosystem was constructed in hydroponic solution by regulating the amounts of organic fertiliser and soil, with moderate aeration. The microbial ecosystem mineralised organic nitrogen to nitrate-nitrogen via ammonification and nitrification. A 97.6% efficiency of nitrate-nitrogen generation from the organic nitrogen in the organic fertiliser was achieved. The culture solution containing the microbial ecosystem was usable as a hydroponic solution. Vegetable plants grew well in our organic hydroponics system under continuous addition of organic fertiliser, and the yield and quality approximated those of vegetables grown by conventional hydroponics.
Temperature factor analysis of outer membrane β-stranded porin crystal structures suggests the pore is not uniformly rigid
Authors: Krishnaswamy S. , Kumar Abhishek 
Published: July 2019

AbstractOuter membrane beta-stranded porins form a diverse and complex set of proteins which allow passage of molecules across the membrane interface have been analyzed here from a biophysical and structural perspective using atomic temperature factors or B-factors. Generally atomic temperature factors of molecules from crystal structures indicate the degree of mobility or disorder seen in the crystal structure. Structures of six porins (four 16 stranded beta barrel porins and two 8 stranded beta barrel porins) were taken from the PDB for the analysis based on resolution (better than 3.0 Å) and R-factor (< 0.23). The residue distribution and mobility distribution was found to be characteristic of each of the porins. The mobility and residue distribution amongst the secondary structural elements were found to follow the level of homology at the sequence and structural level. The loops (L2 and L3) that had defined functional roles in structural terms were found to have lower temperature factors than the other loops. The turn regions that are thought to face the periplasmic region in the cell, showed higher temperature factors. For both the 16 stranded and the 8 stranded barrels it was found one part of the barrel (the lower wall or 'inner' wall comprising the trimer interface in the case of the 16 stranded barrels) was more rigid and the other half of the barrel (the higher or 'outer' wall) showed more mobility as seen from the temperature factors. This seems to be an intrinsic structural component of the beta barrels.
Spatiotemporal dynamics of complex ecological networks: Power-law scaling and implications for conservation planning
Authors: Wright Christopher 
Published: July 2019

AbstractSpatial constraints on the topology of complex networks are just beginning to be appreciated, both theoretically and in concrete examples like the Internet and global air transportation network. Ecological networks, composed of habitat patches connected by species dispersal, are intrinsically spatial and show promise as a tool for conservation planning; but while habitat-loss effects on ecological networks have been simulated, such effects have not been directly measured in ecological networks varying over time. In this study, I used satellite remote sensing to study ecological networks composed of wetland habitat in the Prairie Pothole Region (PPR) of North America. I find power-law scaling of important topological properties as a function of dispersal ability and as wetland density varies with climate. Prairie wetland networks are 'meso-worlds' with mean topological distance increasing faster with network size than small-world networks, but slower than regular lattices. While similar dynamics have been shown in random spatial networks, these results emphasize the importance of processes determining locations of nodes in a spatial network, with possible implications in other areas like wireless communication networks or disease transmission networks. Wetland networks establish a climate envelope for landscape connectivity in the PPR, and I show that wetland-dependent species face a 'crisis of connectivity' with climate change. The global biodiversity crisis requires that conservation planners act quickly over large areas using limited resources; a network-based approach to coarse-filter conservation planning in dynamic landscapes should be broadly applicable to this problem.
Adenovirus-mediated transfer of siRNA against survivin enhances the radiosensitivity of human non-small cell lung cancer cells
Authors: Yang Cheng-Ta , Li Jhy-Ming , Weng Hsu-Huei , Li Ya-Chin , Chen Miao-Fen 
Published: July 2019

AbstractExpression of survivin has been reported to be correlated with shorter survival in patients with non-small cell lung cancer (NSCLC), and overexpression of survivin may lead to radioresistance in various human cancers. In this study, we inhibited survivin expression by using an adenoviral vector (AdsiSurvivin)-mediated RNAi to elucidate the combined effect of survivin-targeting gene therapy and radiotherapy on the NSCLC cells. Our data revealed that AdsiSurvivin exerted survivin gene silencing, induced apoptosis, and significantly attenuated the growth potential in NSCLC cells within 72 hours after infection. The combined treatment modalities with AdsiSurvivin infection and radiation were significantly more potent on cell-growth inhibition than monotherapy. In H1650, H460, A549, and H1975 human NSCLC cells, the survival ratios of AdsiSurvivin-treated groups at m.o.i. of 25 and 50 were significantly lower than those of control groups at varying radiation dose (0~8 Gy; three-way ANOVA, p &lt; 0.05). The cytotoxicity of combined AdsiSurvivin infection and irradiation increased in a dose-dependent manner in both the virus and the irradiation treatment. Knockdown of the survivin gene expression appears to be a promising treatment strategy for NSCLC. Our data warrants the need for further effort to develop survivin-targeted radiosensitizer for lung cancer treatment.
Evidence of existence of totally different types of ribosomes in intermediate animals
Authors: Wang Haoran , Gao Mary , Kenzo Sato , Hirai Kazumitsu 
Published: July 2019

AbstractIn all organisms, messenger-directed protein synthesis is catalyzed by ribonucleoprotein particles called ribosomes. A ribosome is typically composed of one small and one large subunit which contain one short (18S) and one long (28S) rRNAs, respectively. Surprisingly, in this study, three similar size rRNAs (18-21S) were revealed in the electrophoresis profile of the total RNAs of tapeworm Spirometra erinaceiuropaei. Northern blot analysis shows that one of the three bands belongs to 18S rRNA, and the other two bands are of 28S rRNAs, implying structurally distinct ribosomes in this intermediate animal. Furthermore, similar, but not identical profiles were observed in two other tapeworms Diphyllobothrium hottai and Diphyllobothrium Nipponkaiizeme. Relevant to this finding, in flatworm Paragonimus westermani, 18S rRNAs were found much more numerous than 28S rRNAs. Moreover, consistent with this biochemical finding, transmission electron microscopy examinations show that the ribosomes isolated from Spirometra erinaceiuropaei are composed of either one ball or two similar size subunits (balls), while the structure of ribosomes isolated from control liver tissue exactly match the conventional large and small subunit ribosome model. Our study provides direct biochemical and biophysical evidence of structurally distinct novel type of ribosomes in intermediate eukaryotic flatworms. These finding may be important for re-recognition of biological protein synthesis and evolutionary process of living things.
Novel mutations in the toll like receptor genes cause hyporesponsiveness to Mycobacterium avium subsp. paratuberculosis infection
Authors: Bhide Mangesh , Mucha Rastislav , Mikula Ivan , Kisova Lucia , Skrabana Rostislav , Novak Michal , Mikula Ivan 
Published: July 2019

AbstractToll like receptors play a central role in the recognition of pathogen associated molecular patterns (PAMPs). Mutations in TLR1, TLR2 and TLR4 genes may change the PAMP reorganization ability which causes altered responsiveness to the bacterial pathogens. A case control study, performed to assess the association between TLR gene mutations and susceptibility to Mycobacterium avium subsp. paratuberculosis (MAP), revealed novel mutations (TLR1 - Ser150Gly and Val220Met; TLR2 - Phe670Leu) that hindered either PAMP recognition or further downstream TLR pathway activation. A cytokine expression experiments (IL-4, IL-8, IL-10, IL-12 and IFN-&x03B3;) in the challenged mutant and wild type moDCs (mocyte derived dendritic cells) confirmed the negative impact of these mutations and altered TLR downstream activation. Further In silico analysis of the TLR1 and TLR4 ectodomains (ECD) revealed the polymorphic nature of the central ECD and irregularities in the central LRR motifs. The most critical positions that may alter the pathogen recognition ability of TLR were: the 9th amino acid position in LRR motif (TLR1, LRR10) and 4th residue downstream to LRR domain (exta LRR region of TLR4). The study describes novel mutations in the TLRs and presents their association with the MAP infection.
Trophoblastic hormones direct early human embryogenesis
Authors: Gallego Miguel , Porayette Prashob , Kaltcheva Maria , Bowen Richard , Vadakkadath Meethal Sivan , Atwood Craig 
Published: July 2019

AbstractDivision of the human zygote leads to the formation of the blastocyst that contains human embryonic stem cells (hESC) which develop into the embryo. Little is known about the physiological signals that direct hESC division and differentiation during early embryogenesis. A number of growth factors, including the pregnancy-associated hormone human chorionic gonadotropin (hCG), are secreted by trophoblasts^1-3^ that lie adjacent to the embryoblast in the blastocyst, but it is not known whether these growth factors directly signal the epiblast. Here we show that hCG promotes the division of embryoblast-derived inner mass cells (hESC), and their differentiation during blastulation and neurulation. Inhibition of LH/hCG receptor (LHCGR) signaling with P-antisense oligonucleotides suppresses hESC proliferation. Similarly, hESC proliferation can be blocked using an antibody against the extracellular activation site of LHCGR, an effect that is reversed by treatment with hCG. hCG treatment rapidly upregulates steroidogenic acute regulatory protein-mediated cholesterol transport and the synthesis of progesterone, a neurogenic steroid^4,5^. Treatment of hESC colonies with progesterone induces neurulation as demonstrated by the expression of nestin and the formation of columnar neuroectodermal cells that organize into neural tube-like rosettes. Suppression of progesterone signaling by withdrawing progesterone or treating with the progesterone receptor antagonist RU-486 inhibits the differentiation of hESC colonies into embryoid bodies (blastulation) and rosettes (neurulation). These results explain the default pathway of hESC differentiation towards a neural stem cell fate in vitro. Collectively, our findings implicate trophoblastic hCG secretion and signaling via LHCGR on the adjacent embryoblast in the induction of hESC proliferation and differentiation into blastocysts and neurula. This paracrine/juxtacrine signaling by extraembryonic tissues is the commencement of trophic support by placental tissues in the growth and development of the human embryo.
Kinetic control of eukaryotic chromatin structure by recursive topological restraints
Authors: Borek Dominika , Otwinowski Zbyszek 
Published: July 2019

AbstractChromatin structure undergoes many changes during the cell cycle and in response to regulatory events. A basic unit of chromatin organization is the nucleosome core particle. However, very little is known about how nucleosomes are arranged into higher-order structures in vivo, even though the efficiency and precision of cell division imply high levels of structural organization. We propose abandoning the current paradigm of chromatin organization based on thermodynamics of the lowest energy state and replace it with the idea of a topologically restrained, high-energy structure. We propose that DNA is subject to a recursive topological restraint, and is anchored by hemicatenates that are part of the chromosomal scaffold. Long-distance cis-regulation of transcription is a natural consequence of recursive topological restraint. This new theory of chromatin structure has a multitude of consequences for key aspects of cellular biology.
Anhedonia in the shadow of chronic social defeat stress, or When the experimental context matters
Authors: Bondar Natalia P. , Kovalenko Irina L. , Avgustinovich Damira F. , Smagin Dmitry A. , Kudryavtseva Natalia N. 
Published: July 2019

AbstractOne of the core symptoms of major depression in human is anhedonia. For that reason, one of the main requirements towards experimental depression models is that they be able to demonstrate anhedonia in animals, that have been exposed to stressful events, and other behavioral changes attributable to a depression-like state. However, the results presented in the literature are contradictory: sweet solution intake, which is considered as a parameter of hedonic/anhedonic behavior in animals, responds quite differently to stressful situations in that it is either unaffected or increased or decreased. Different experimental designs used for the study of anhedonia in male mice exposed to chronic social defeat stress were tried to understand the reasons for so contradictory responses. Anhedonia appears as an abrupt reduction in sweet solution consumption in stressed animals and by failure to attain recovery after deprivation. However, it was also demonstrated that sucrose solution intake and preference strongly depend on the experimental context; that the possible critical factor may be prior acquaintance with the hedonic stimulus – or the lack whereof. Analysis of literature data and ours allowed us to conclude that the lack of a significant decrease in sweet solution intake in stressed animals is no evidence of lack of depression. This decrease is evidence of anhedonia only provided other symptoms of depression are present. Hedonic consumable intake can be decreased over various motivations, conditions or diseases, in particular, a high level of anxiety or pathological aggression.
Fundamentally different strategies for transcriptional regulation are revealed by analysis of binding motifs
Authors: Mirny Leonid , Wunderlich Zeba 
Published: July 2019

AbstractTo regulate a particular gene, a transcription factor (TF) needs to bind a specific genome location. How is this genome address specified amid the presence of ~10^6-10^9 decoy sites? Our analysis of 319 known TF binding motifs clearly demonstrates that prokaryotes and eukaryotes use strikingly different strategies to target TFs to specific genome locations; eukaryotic TFs exhibit widespread nonfunctional binding and require clustering of sites in regulatory regions for specificity.
Fundamentally different strategies for transcriptional regulation are revealed by analysis of binding motifs
Authors: Wunderlich Zeba , Mirny Leonid 
Published: July 2019

AbstractTo regulate a particular gene, a transcription factor (TF) needs to bind a specific genome location. How is this genome address specified amid the presence of ~10^6^-10^9^ decoy sites? Our analysis of 319 known TF binding motifs clearly demonstrates that prokaryotes and eukaryotes use strikingly different strategies to target TFs to specific genome locations; eukaryotic TFs exhibit widespread nonfunctional binding and require clustering of sites in regulatory regions for specificity.
Social Processing of Discrete Emotions in Humans
Authors: Vigil Jacob 
Published: July 2019

AbstractI asked human observers to rate capacity and trustworthiness trait impressions of, and to indicate affiliative and avoidant dispositions, and felt emotive responses toward social objects. I show that interpersonal dispositions and emotive responses are systematically associated with variation in perceived levels of these trait impressions. The findings suggest that perception and expression of cues that signal capacity and trustworthiness of reciprocating altruism may underlie discrete affect behaviors in humans.
DNA Genealogy, Mutation Rates, and Some Historical Evidences Written in Y-Chromosome
Authors: Klyosov Anatole 
Published: July 2019

AbstractOrigin of peoples in a context of DNA genealogy is an assignment of them to a particular tribe (all members of which belong to a certain haplogroup) or its branch (a lineage), initiated in a genealogical sense by a common ancestor and an estimation of a time span between the common ancestor and its current descendants. We have developed an approach to kinetics of haplotype mutations in non-recombinant segments of the Y-chromosome and illustrated it with a number of haplotype series related to various populations (timespans to common ancestors shown as years before the present): Basques R1b1b2 (4,050), near thirty of European countries R1a1 (between 4,100 and 4,825), India R1a1 (3,675), the Arabian Peninsula R1a1 (3,750), South India Chenchu R1a1 (3,200 and 350, two lineages), bearers of so-called Cohen Modal Haplotype (CMH) J1 (4,000 and 1,050, two lineages), and CMH J2 (1,400), Arabian CMH J1 (9,000), Bulgarian and Croatian Gypsies H1 (575 and 1,125, respectively), Polynesians C2 (800), South African Lemba (625), the oldest Balkan R1a1 population (11,600), and Native Americans Q (16,000). Some of these findings are supported by independent estimates.
Computational methods in cancer gene networking
Authors: Wang Edwin 
Published: July 2019

AbstractIn the past few years, many high-throughput techniques have been developed and applied to biological studies. These techniques such as “next generation” genome sequencing, chip-on-chip, microarray and so on can be used to measure gene expression and gene regulatory elements in a genome-wide scale. Moreover, as these technologies become more affordable and accessible, they have become a driving force in modern biology. As a result, huge amount biological data have been produced, with the expectation of increasing number of such datasets to be generated in the future. High-throughput data are more comprehensive and unbiased, but ‘real signals’ or biological insights, molecular mechanisms and biological principles are buried in the flood of data. In current biological studies, the bottleneck is no longer a lack of data, but the lack of ingenuity and computational means to extract biological insights and principles by integrating knowledge and high-throughput data. Here I am reviewing the concepts and principles of network biology and the computational methods which can be applied to cancer research. Furthermore, I am providing a practical guide for computational analysis of cancer gene networks.