bluuebunny/crossref_metadata_2025_split huggingface dataset:
On the Doubly hydrogen bonded dimer of 7-azaindole (0.1 M) as a model for DNA base pairs in acetonitrile solutions at rt
Authors: Catalan Javier 
Published: July 2019

AbstractMultiple H-bonded base-pairing as a fundamental element of DNA structure was first described by Watson and Crick using stable keto tautomer forms. In their analysis, they considered the possibility of mutations via tautomeric proton transfer shifts. Among other phenomena, such shifts can be caused by electronic excitation; for example, anomalous adenine-cytosine pairing may be a result of two-proton phototautomerism. One suitable model base pair for two-proton translocating tautomerization is the C2h dimer of 7-azaindole (7AI) proposed by Taylor et al. in 1969. The most salient contribu&x00AC;tion of their work was that the double proton transfer in such a dimer occurs in a concerted manner. After the strong controversy raised in 1995 by the proposal of Douhal et al. of a stepwise mechanism for the process was overcome, its concerted nature has been strongly supported by available evidence (see references and references therein). Very recently, however, Kwon and Zewail claimed to have obtained new supportive evidence that the proton phototransfer in 7AI dimer in polar solvents is in fact a stepwise rather than concerted process. In this communication, we conducted a systematic spectroscopic study of the dimerization of 7AI at a 0.1 M concentration in acetonitrile that may allow us to demonstrate whether the 0.1 M 7AI solutions in acetonitrile at room temperature used by Kwon and Zewail contained enough 7AI doubly hydrogen bonded dimer to enable its photoselection and hence its photophysical characterization with femtosecond / fluorescence spectroscopy.
MR Neurography and Diffusion Tensor Imaging: Origin, History and Impact
Authors: Filler Aaron 
Published: July 2019

Abstract
Objective
– Methods were invented that made it possible to image peripheral nerves in the body and to image neural tracts in the brain. Over a 15 year period, these techniques – MR Neurography and Diffusion Tensor Imaging – were then deployed in the clinical and research community and applied to about 50,000 patients. Within this group, about 5,000 patients having MR Neurography were carefully tracked on a prospective basis.

Method
– In the study group a uniform imaging methodology was applied and all images were reviewed and registered by referral source, clinical indication, efficacy of imaging and quality. Various classes of image findings were identified and subjected to a variety of small targeted prospective outcome studies. Those findings demonstrated to be clinically significant were then tracked in the larger clinical volume data set.

Results
– MR Neurography demonstrates mechanical distortion of nerves, hyperintensity consistent with nerve irritation, nerve swelling, discontinuity, relations of nerves to masses, and image features revealing distortion of nerve at entrapment points. These findings are often clinically relevant and warrant full consideration in the diagnostic process. They result in specific pathologic diagnoses that are comparable to electrodiagnostic testing in clinical efficacy.

Conclusions
– MR Neurography and DTI neural tract imaging have been validated as indispensable clinical diagnostic methods that provide reliable anatomical pathological information. There is no alternative diagnostic method in many situations. With the elapse of 15 years, tens of thousands of imaging studies, and hundreds of publications, these methods should no longer be considered experimental.
MR Neurography and Diffusion Tensor Imaging: Origin, History and Impact
Authors: Filler Aaron 
Published: July 2019

Abstract
*Objective:*
Methods were invented that made it possible to image peripheral nerves in the body and to image neural tracts in the brain. Over a 15 year period, these techniques – MR Neurography and Diffusion Tensor Imaging – were then deployed in the clinical and research community and applied to about 50,000 patients. Within this group, about 5,000 patients having MR Neurography were carefully tracked on a prospective basis.*Method:* In the study group a uniform imaging methodology was applied and all images were reviewed and registered by referral source, clinical indication, efficacy of imaging and quality. Various classes of image findings were identified and subjected to a variety of small targeted prospective outcome studies. Those findings demonstrated to be clinically significant were then tracked in the larger clinical volume data set.

*Results:*
MR Neurography demonstrates mechanical distortion of nerves, hyperintensity consistent with nerve irritation, nerve swelling, discontinuity, relations of nerves to masses, and image features revealing distortion of nerve at entrapment points. These findings are often clinically relevant and warrant full consideration in the diagnostic process. They result in specific pathologic diagnoses that are comparable to electrodiagnostic testing in clinical efficacy.

*Conclusions:*
MR Neurography and DTI neural tract imaging have been validated as indispensable clinical diagnostic methods that provide reliable anatomical pathological information. There is no alternative diagnostic method in many situations. With the elapse of 15 years, tens of thousands of imaging studies, and hundreds of publications, these methods should no longer be considered experimental.
A common subcortical oscillatory network contributes to recovery after spinal cord injury
Authors: Nishimura Yukio , Morichika Yosuke , Isa Tadashi 
Published: July 2019

AbstractRecent studies in monkeys showed that when the direct cortico-motoneuronal connection was transected at mid-cervical segments, remaining, indirect cortico-motoneuronal pathways compensated for finger dexterity within one to three months. To elucidate the changes in dynamic properties of neural circuits during the recovery, we investigated the cortico-muscular and inter-muscular couplings of activities throughout the recovery course. Activities of antagonist muscle pairs showed co-activation during the second postoperative week, and oscillated coherently at frequencies of 30-46 Hz (gamma-band) by one month postoperatively. Such gamma-band inter-muscular coherence was not observed preoperatively, but became prominent and distributed widely over proximal and distal muscles with the recovery. Neither the gamma-band cortico-muscular coupling (14-30 Hz) observed before lesion, nor a gamma-band oscillation was observed in bilateral motor cortex after lesion. Thus, we propose that an unknown, subcortical oscillator, independent of cortical oscillation, commonly recruits hand/arm muscles and may underlie functional recovery of dexterous finger movements.
On the Coding of Negative Quantities in Cortical Circuits
Authors: Ballard Dana , Jehee Janneke 
Published: July 2019

AbstractMullers Law of specific nerve energies introduced the idea that nerves transmit information about specific sensory features. This concept has been refined by the notion of 'labeled lines,' specific cells that capture sub-features of a sensory or motor stimulus, such as Hubel and Weisel's opponent color cells. Such features can be visualized as coding a signed quantity that has positive and negative components that are encoded with separate nerve cells. We show that there are two important consequences when learning receptive field using signed codings in circuits. The first is that in feedback circuits even simple operations need to be distributed across multiple distinct pathways. The second consequence is that such pathways are necessarily dynamic. Synaptic weights change during learning and must break and grow new circuit connections because the weights need to change sign during receptive field formation.
Function, Role, and Disposition in Basic Formal Ontology
Authors: Arp Robert , Smith Barry 
Published: July 2019

AbstractNumerous research groups are now utilizing Basic Formal Ontology (BFO) as an upper-level framework to assist in the organization and integration of biomedical information. This paper provides elucidation of the three BFO categories of function, role, and disposition, and considers two proposed sub-categories of artifactual function and bio-logical function. The motivation is to help advance the coherent treatment of functions, roles, and dispositions, to help provide the potential for more detailed classification, and to shed light on BFO’s general structure and use.
11-amino-5-N-methyl-7-fluorine- quindoline derivatives: The Potential Anti-angiogenic Agents Targeting G-quadruplex Structure in Vascular Endothelial Cell Growth Factor
Authors: Ou Tian-miao , Lu Yu-jing , Wang Xiao-dong , An Zeng-yun , Li Yan-ping , Huang Zhi-shu , Gu Lian-quan 
Published: July 2019

AbstractVascular endothelial growth factor (VEGF), a pluripotent cytokine and angiogenic growth factor, plays crucial roles in embryonic development and tumour progression, and is over-expressed in many types of cancer and generally associated with tumour progression and survival rate. The polypurine/polypyrimide sequence located upstream (-89 to -43) of the promoter region of the human VEGF gene that can form specific G-quadruplex structures and raise the possibility for transcriptional control of the VEGF gene by G-quadruplex ligands. In the present study, we investigated the interaction between the 5-N-methyl-7-fluorine-quindoline derivatives (11-amino-5-N-methyl-7-fluorine- quindoline derivatives) and the G-rich sequence in VEGF&apos;s promoter and the subsequent effects on the biological functions of VEGF. We found the strong interaction between the 5-N-methyl-7-fluorine-quindoline derivatives and the G-rich DNA of VEGF, and this interaction might significantly influence the biological functions of VEGF, including the transcription and expression of VEGF, cell proliferation and apoptosis, and the stimulation of angiogenesis in chick embryo.
An experimental and modelling exploration of the host-sanction hypothesis in legume-rhizobia mutualism
Authors: Marco Diana , Carbajal Juan , Cannas Sergio , Perez-Arnedo Rebeca , Hidalgo-Perea Angeles , Olivares Jose , Ruiz-Sainz Jose , Sanjuán Juan 
Published: July 2019

AbstractDespite the importance of mutualism as a key ecological process, its persistence in nature is difficult to explain since the existence of exploitative, 'cheating' partners that could erode the interaction is common. By analogy with the proposed policing strategy stabilizing intraspecific cooperation, host sanctions against non N2 fixing, cheating symbionts have been proposed as a force stabilizing mutualism in legume-Rhizobium symbiosis. Following this proposal, penalizations would include decreased nodular rhizobial viability and/or early nodule senescence in nodules occupied by cheating rhizobia. In this work, we analyze the stability of Rhizobium-legume symbiosis when "cheating" strains are present, using an experimental and modelling approach. We used split-root experiments with soybean plants inoculated with two rhizobial strains, a cooperative, normal N2 fixing strain and an isogenic non-fixing, “perfect” cheating mutant derivative that lacks nitrogenase activity but has the same nodulation abilities inoculated to split-root plants. We found no experimental evidence of functioning plant host sanctions to cheater rhizobia based on nodular rhizobia viability and nodule senescence and maturity molecular markers. Based on these experiments, we developed a population dynamic model with and without the inclusion of plant host sanctions. We show that plant populations persist in spite of the presence of cheating rhizobia without the need of incorporating any sanction against the cheater populations in the model, under the realistic assumption that plants can at least get some amount of fixed N2 from the effectively mutualistic rhizobia occupying some nodules. Inclusion of plant sanctions merely reduces the time needed for reaching plant population equilibrium and leads to the unrealistic effect of ultimate extinction of cheater strains in soil. Our simulation results are in agreement with increasing experimental evidence and theoretical work showing that mutualisms can persist or even improve in presence of cheating partners.
Reinforcement learning in populations of spiking neurons
Authors: Urbanczik Robert , Senn Walter 
Published: July 2019

AbstractPopulation coding is widely regarded as a key mechanism for achieving reliable behavioral responses in the face of neuronal variability. But in standard reinforcement learning a flip-side becomes apparent. Learning slows down with increasing population size since the global reinforcement becomes less and less related to the performance of any single neuron. We show that, in contrast, learning speeds up with increasing population size if feedback about the populationresponse modulates synaptic plasticity in addition to global reinforcement. The two feedback signals (reinforcement and population-response signal) can be encoded by ambient neurotransmitter concentrations which vary slowly, yielding a fully online plasticity rule where the learning of a stimulus is interleaved with the processing of the subsequent one. The assumption of a single additional feedback mechanism therefore reconciles biological plausibility with efficient learning.
Structural basis of the allosteric trigger of the Hsp70 chaperone proteins.
Authors: Bhattacharya Akash , Kurochkin Alexander , Yip Grover , Bertelsen Eric , Zuiderweg Erik 
Published: July 2019

AbstractThis work solves a decades-old dilemma that stood in the way of understanding the allosteric mechanism of Hsp70 (heat shock 70 kDa) chaperone proteins. Hsp70s are central to protein folding, refolding, and trafficking in organisms ranging from Archae to Homo Sapiens, both at normal and at stressed cellular conditions. Hsp70s are comprised of two main domains: a 44 kDa N-terminal nucleotide-binding domain (NBD), and a 25 kDa substrate-binding domain (SBD) that harbors the substrate binding site. The nucleotide binding site in the NBD and the substrate binding site in the SBD are allosterically linked: ADP binding promotes substrate binding, while ATP binding promotes substrate release. It has long been a goal of structural biology to characterize the nature of the allosteric coupling in these proteins. However, even the most sophisticated X-ray crystallography studies of the isolated NBD could show no difference in overall conformation between the ATP and ADP state. Hence the dilemma: how is the state of the nucleotide communicated between NBD and SBD? The solution of the dilemma is especially interesting in light of the fact that Hsp70s are ancient proteins, and amongst the first allosteric proteins in nature.Here we report a solution NMR study of the NBD of the Hsp70 from Thermus thermophilus, in the APO, ADP and AMP-PNP states, where the latter is a non-hydrolysable ATP analogue. Using the modern NMR methods of residual dipolar coupling analysis, we discovered that the nucleotide binding cleft opens up by as much as 20 degrees between the AMP-PNP (closed) and ADP (open) state. We also discover that a surface cleft, hypothesized to be essential for the allosteric coupling between NBD and SBD, echoes these changes. Hence, the nature of the allosteric trigger and coupling for Hsp70 chaperones is revealed here for the first time, solving the dilemma.
Is the innate bio-protection power against human virus the same between males and females? A conclusion based on blood donor data of HTLV-I infection and case data of infectious diseases
Authors: Eshima Nobuoki , Tabata Minoru , Higuchi Yasunori , Karukaya Shigeru 
Published: July 2019

AbstractHuman T-cell leukemia virus type I (HTLV-I) is a retrovirus that causes adult T-cell leukemia. The male-to-female transmission is stronger than the reverse, so the carrier proportion of women is greater than that of men. On the other hand, since the mother-to-child transmission route via the breast-feeding is common for baby boys and girls, it has been thought the HTLV-I proportions of boys and girls are the same until now. A question arises as to whether the ‘innate protection powers against human virus’ are the same between males and females. We utilize HTLV-I infection blood donor data in 1995-1998 and case data of main infectious diseases such as influenza, mumps, herpangina, hand-hoot-and-mouse disease, chicken pox, etc. Blood donor data in 1995-1998, which were provided by Japan Red Cross Society of Oita, Japan, are summarized into the frequency table with respect to gender and age. The age groups are < 20, 20 < age , 30 < age , 40 < age , and > 50 years old. The comparison of carrier proportions of males and females under 20 years old is made with a two-sided statistical test and for the other groups one-sided tests are carried out. In case data published from the National Institute of Infectious Diseases, Japan, comparisons of the incidence rates of males and females in infectious diseases are carried out with two-sided tests. The present paper shows that the HTLV-I carrier proportion of girls is less than that that of boys. It implies that in HTLV-I the mother-to-child transmission probability of females is less than that of males. With respect to the other main infectious diseases, the majority of cases are under twenty years old, and the incidence rates of females are also significantly less than those of males. According to the present findings, it follows that the female’s innate protection power against HTLV-I is stronger than that of males, and the conclusion may become a valid proposition for general human virus.
Population genomics of domestic and wild yeasts
Authors: Carter David , Liti Gianni , Moses Alan , Parts Leopold , James Stephen , Davey Robert , Roberts Ian , Blomberg Anders , Warringer Jonas , Burt Austin , Koufopanou Vassiliki , Tsai Isheng , Bergman Casey , Bensasson Douda , O’Kelly Michael , van Oudenaarden Alexander , Barton David , Bailes Elizabeth , Jones Matthew , Quail Michael , Goodhead Ian , Sims Sarah , Smith Frances , Durbin Richard , Louis Edward 
Published: July 2019

AbstractThe natural genetics of an organism is determined by the distribution of sequences of its genome. Here we present one- to four-fold, with some deeper, coverage of the genome sequences of over seventy isolates of the domesticated baker's yeast, Saccharomyces cerevisiae, and its closest relative, the wild S. paradoxus, which has never been associated with human activity. These were collected from numerous geographic locations and sources (including wild, clinical, baking, wine, laboratory and food spoilage). These sequences provide an unprecedented view of the population structure, natural (and artificial) selection and genome evolution in these species. Variation in gene content, SNPs, indels, copy numbers and transposable elements provide insights into the evolution of different lineages. Phenotypic variation broadly correlates with global genome-wide phylogenetic relationships however there is no correlation with source. S. paradoxus populations are well delineated along geographic boundaries while the variation among worldwide S. cerevisiae isolates show less differentiation and is comparable to a single S. paradoxus population. Rather than one or two domestication events leading to the extant baker's yeasts, the population structure of S. cerevisiae shows a few well defined geographically isolated lineages and many different mosaics of these lineages, supporting the notion that human influence provided the opportunity for outbreeding and production of new combinations of pre-existing variation.
Mechanisms to overcome ecosystem nitrogen and phosphorus limitation
Authors: Ostertag Rebecca 
Published: July 2019

AbstractNutrients limit plant growth in many ecosystems, and many species develop adaptations to either obtain more nutrients or to avoid losses. Much past ecological work has focused either on temperate nitrogen-limited systems or has addressed infertile soils as a single entity, rather than addressing the nature of the limitation. Although low nitrogen (N) and phosphorus (P) soils are found worldwide, the consequences of N and P limitation for plants may vary due to fundamental differences in the soil mobility, availability, uptake, and cellular uses of N and P. Using a well-studied chronosequence in the Hawaiian Islands, which contains both low N and P soils but which is dominated by similar plant communities, foliar N and P plant responses to fertilization were examined across a diverse group of species and life forms. Here it is shown that in response to N fertilization, foliar N concentrations do not significantly increase. In contrast, P fertilization leads to highly elevated foliar P concentrations and lower N:P values. This accumulation of P is evident across all species, occurs regardless of site fertility, results in increased concentrations of P in both inorganic and organic forms, and may be highly advantageous due to the patchy nature of soil P availability. Results indicate that greater variation in foliar P than foliar N after fertilization transcends soil nutrient availability and may be widespread among ecosystems. Such P accumulation means that N and P concentrations may not be in close association after pulses of soil P. It also provides a mechanism whereby ecosystem P limitation may be overcome with external inputs more easily than N limitation and points for the need to think about N and P limitation not just as infertile stressful conditions for plants, but as two fundamentally different phenomena.
In vivo evidence for NMDA receptor mediated excitotoxicity in a murine genetic model of Huntington Disease
Authors: Heng Mary , Detloff Peter , Wang Phillip , Tsien Joe , Albin Roger 
Published: July 2019

AbstractN-methyl-D-aspartate receptor (NMDAR) mediated excitotoxicity is implicated as a proximate cause of neurodegeneration in Huntington Disease (HD). However, this hypothesis has not been tested rigorously in vivo. NMDAR NR2B-subunits are the predominant NR2 subunit expressed by the striatal medium spiny neurons that degenerate in HD. To test this hypothesis, we crossed a well validated murine genetic model of HD (Hdh(CAG)150) with a transgenic line overexpressing NMDAR NR2B-subunits. In the resulting double mutant line, we show exacerbation of selective striatal neuron degeneration. These results provide the first direct in vivo evidence of NR2B-NMDAR mediated excitotoxicity in the context of HD. Our results are consistent with prior suggestions that direct and/or indirect interactions of mutant huntingtin with NMDARs are a proximate cause of neurodegeneration in HD.