bluuebunny/crossref_metadata_2025_split huggingface dataset:
The hypothesis of basic phenotype modules
Authors: von Zelewsky Thomas 
Published: July 2019

AbstractThe evolutionary events that allowed the rapid occurrence of metazoa are still enigmatic. The presumably oldest metazoan fossils are microscopic and occur just above 635 Ma, at the beginning of the Ediacaran period. Upon condition that the lack of macrofossils in the lower Ediacaran strata is real, the assumption of a sudden appearance of already complex, but still small animals that flourished during the first half of the Ediacaran is a reasonable option. Consequently, the emergence of the first macrofossils with metazoan affinity in mid Ediacaran strata would indicate a second leap in animal evolution. Here, these apparent leaps are explained in terms of a new concept of evolvability that is based on well definable developmental modules: A system based on blast cell-induced cell division modules has paved the way for rapid evolution to small multicellular animals. The second module, an ancestral form of segments, allowed the construction of a new sort of metameric body plans that appeared some tenth of million years later and at a larger scale. Based on this new model of basic radiations, the lower Ediacaran strata are predicted to contain a sequence of exotic embryos that is followed by an explosion of small metazoan diversity. The upper Ediacaran biota are interpreted as representatives of an evolutionary succession that culminated in a maximally evolvable and segmented ancestor with an already complex archetype body plan. Then, around the Ediacaran-Cambrian boundary branching of most modern animal phyla would have taken place, with extensive secondary simplifications in many groups. This radically new hypothesis allows the formulation of clear predictions that are in agreement with available fossils and geochemical data from that period, however, it calls for a precise and chronologically well-definable sequence of Ediacaran events that can only be confirmed through future investigations.
Molecular Evaluation of exons 8 and 22 of the SHANK3 gene in Autism Spectrum Disorders
Authors: Bossolani-Martins A , Rodrigues-Lisoni F , Nogueira M , Barbosa-Gonçalves A , Tajara E , Fett-Conte A 
Published: July 2019

AbstractAutism spectrum disorders are a group of neurodevelopmental disorders with a complex and heterogeneous etiology. Studies have shown that genetic factors play an important role in the aetiology of these diseases. Recently, de novo mutations, frameshifts and deletions have been described in the SHANK3 gene, also known as ProSAP2 gene, which encodes a synaptic scaffolding protein. All the participants of this study had normal karyotypes and underwent screening for Fragile-X syndrome. Subsequently, they were analyzed by direct sequencing of different points of exons 8 and 22 of the SHANK3 gene. None of the study participants presented with changes in these regions. These findings may be due to the fact that mutations, deletions and duplications of the SHANK3 gene are rare.
Origin of the Jews and the Arabs: Date of their Most Recent Common Ancestor is Written in their Y-Chromosomes - However, There Were Two of Them
Authors: Klyosov Anatole 
Published: July 2019

AbstractA pattern of Y-chromosomal mutations in 37 and 67 marker haplotypes of the Jews and the Arabs indicates that their most recent common ancestor in haplogroup J1 (subclade J1e*) and that (a different one) in haplogroup J2 (subclade J2a*) lived 4300+/-500 years before present (ybp) and 4175+/-510 ybp, respectively, that is practically at the same time. Then a split between the Jewish and the Arabic lineages in both J1 and J2 haplogroups occurred, which is clearly visible on the respective haplotype trees. The data show that a common ancestor of Cohanim (Jewish High Priests) of haplogroup J1 lived 1070+/-170 ybp, while a common ancestor of Cohanim in haplogroup J2 lived 3300+/-400 ybp.
A schistosome [beta] subunit remodels inactivation of a calcium channel via an N-terminal polyacidic motif
Authors: Salvador-Recatala Vicenta , Greenberg Robert 
Published: July 2019

AbstractThe beta subunit of high voltage-activated Ca (Cav) channels targets the pore forming [alpha]~1~ subunit to the plasma membrane and defines the biophysical phenotype of the Cav channel complex. Cav channel inactivation following activation and opening is tightly regulated and is an essential property that not only prevents excessive entry of Ca^2+^ into the cell but may also have functions in signal transduction. The [beta] subunit modulates Ca^2+^-dependent and voltage-dependent components of Cav channel inactivation via its interaction with the I-II linker of the [alpha]~1~ subunit. Here, using Cav2.3 and whole-cell patch-clamp, we show that a [beta] subunit from the human parasite Schistosoma mansoni ([beta]~Sm~) accelerates inactivation via a unique, long N-terminal polyacidic motif (NPAM). The accelerating effect of NPAM-containing subunits, both native ([beta]~Sm~)and chimeric mammalian [beta]~1b~, [beta]~2a~ and [beta]~3~ subunits to which NPAM had been attached, was only apparent when Ca^2+^ was internally buffered with BAPTA (5 mM) or when Ba^2+^ was used as the charge carrier, two commonly used strategies to eliminate Ca^2+^/calmodulin dependent inactivation. These results indicate that calmodulin is not involved. In addition to accelerating inactivation, NPAM-containing [beta] subunits significantly reduced current density with respect to their non NPAM-bearing counterparts. Interestingly, when the amino acids N terminal to NPAM were deleted, inactivation of Cav2.3 currents was faster than in the presence of the entire N-terminal portion of the [beta]~Sm~ subunit, as if the pre-NPAM region counteracts the effect of NPAM. Presence of NPAM also resulted in currents that activated faster, suggesting that NPAM increases open channel probability. However, NPAM does not modulate inactivation gating. In summary, this study identifies a structural determinant of Cav channel inactivation that is entirely unlike those previously known.
Neuroscience and eating disorders: the role of the medial temporal lobe
Authors: Riva Giuseppe 
Published: July 2019

AbstractEvidence from psychology and neuroscience indicates that our spatial experience, including the bodily one, involves the integration of different sensory inputs within two different reference frames egocentric (body as reference of first-person experience) and allocentric (body as object in the physical world). Even if functional relations between these two frames are usually limited, they influence each other during the interaction between long- and short-term memory processes in spatial cognition. If, for some reasons, this process is impaired, the egocentric sensory inputs are no more able to update the contents of the allocentric representation of the body: the subject is locked to it.In our perspective, subjects with eating disorders are locked to an allocentric representation of their body, stored in long-term memory. A significant role in the locking may be played by the medial temporal lobe, and in particular by the connection between the hippocampal complex and amygdala.
A stem-cell ageing hypothesis on the origin of Parkinson's disease
Authors: Valente André , Sousa Jorge , Outeiro Tiago , Ferreira Lino 
Published: July 2019

AbstractA transcriptome-wide blood expression dataset of Parkinson’s disease (PD) patients and controls was analyzed under the hypothesis-rich mathematical framework. The analysis pointed towards differential expression in blood cells in many of the processes known or predicted to be disrupted in PD. We suggest that circulating blood cells in PD patients can be in a full-blown PD-expression state. We put forward the hypothesis that sporadic PD can originate as a case of hematopoietic stem cell/differentiation process expression program defect and suggest this research direction deserves further investigation.
Using open access literature to guide full-text query formulation
Authors: Piwowar Heather , Chapman Wendy 
Published: July 2019

Abstract
Background
Much scientific knowledge is contained in the details of the full-text biomedical literature. Most research in automated retrieval presupposes that the target literature can be downloaded and preprocessed prior to query. Unfortunately, this is not a practical or maintainable option for most users due to licensing restrictions, website terms of use, and sheer volume. Scientific article full-text is increasingly queriable through portals such as PubMed Central, Highwire Press, Scirus, and Google Scholar. However, because these portals only support very basic Boolean queries and full text is so expressive, formulating an effective query is a difficult task for users. We propose improving the formulation of full-text queries by using the open access literature as a proxy for the literature to be searched. We evaluated the feasibility of this approach by building a high-precision query for identifying studies that perform gene expression microarray experiments. *Methodology and Results* We built decision rules from unigram and bigram features of the open access literature. Minor syntax modifications were needed to translate the decision rules into the query languages of PubMed Central, Highwire Press, and Google Scholar. We mapped all retrieval results to PubMed identifiers and considered our query results as the union of retrieved articles across all portals. Compared to our reference standard, the derived full-text query found 56% (95% confidence interval, 52% to 61%) of intended studies, and 90% (86% to 93%) of studies identified by the full-text search met the reference standard criteria. Due to this relatively high precision, the derived query was better suited to the intended application than alternative baseline MeSH queries. *Significance* Using open access literature to develop queries for full-text portals is an open, flexible, and effective method for retrieval of biomedical literature articles based on article full-text. We hope our approach will raise awareness of the constraints and opportunities in mainstream full-text information retrieval and provide a useful tool for today’s researchers.
Dys-regulated Gene Expression Networks by Meta-Analysis of Microarray Data on Oral Squamous Cell Carcinoma
Authors: Liu Zhongyu , Niu Yulong , Li Chao , Zhou Yang , Yang Yi , Gao Chunfang 
Published: July 2019

Abstract
Background:
Oral squamous cell carcinoma (OSCC) is the sixth most common type of carcinoma worldwide. Development of OSCC is a multi-step process involving genes related to cell cycle, growth control, apoptosis, DNA damage response and other cellular regulators. The pathogenic pathways involved in this tumor are mostly unknown and therefore a better characterization of OSCC gene expression profile would represent a considerable advance. The availability of publicly available gene expression datasets has opened up new challenges especially for the integration of data generated by different research groups and different array platforms with the purpose of obtaining new insights on the biological process investigated.

Results:
In this work we performed a meta-analysis on four microarray and four datasets of gene expression data on OSCC in order to evaluate the degree of agreement of the biological results obtained by these different studies and to identify common regulatory pathways that could be responsible of tumor growth. Sixteen dys-regulated pathways implicated in OSCC were mined out from the four published datasets, and most importantly three pathways were first reported. Those regulatory pathways and biological processes which are significantly enriched have been investigated by means of literatures and meanwhile, four genes of the maximally altered pathways, ECM-receptor interaction, were validated and identified by qRT-PCR as a possible candidate of aggressiveness of OSCC.

Conclusion:
we have developed a robust method for analyzing pathways altered in OSCC using three expression array data sets. This study sets a stage for the further discovery of the basic mechanisms that may underlie a diseased state and would help in identifying critical nodes in the pathway that can be targeted for diagnosis and therapeutic intervention. In addition, those who are interested in our approach can obtain the software package (MATLAB platform) by email freely.
A Rate Distortion approach to protein symmetry
Authors: Wallace Rodrick 
Published: July 2019

AbstractA spontaneous symmetry breaking argument is applied to the problem of protein folding, via a Rate Distortion analysis of the relation between genome coding and the final condensation of the protein molten globule. In the 'energy' picture, the average distortion between codon message and protein structure, under constraints driven by evolutionary selection, serves as a temperature analog, so that low values limit the possible distribution of protein forms, producing the canonical folding funnel. A dual 'developmental' perspective sees the rate distortion function itself as the temperature analog, and permits incorporation of chaperons or toxic exposures as catalysts, driving the system to different possible outcomes or affecting the rate of convergence. The rate distortion function appears constrained by the availability of metabolic free energy, with implications for prebiotic evolution, and a nonequilibrium empirical Onsager treatment provides an adaptable statistical model that can be fitted to data, in the same manner as a regression equation. Mechanistic models of protein folding fail to account for the observed spectrum of folding and aggregation disorders, suggesting that a biologically based cognitive paradigm describing the folding process will be needed for understanding the etiology, prevention, and treatment of these diseases. The developmental formalism introduced here may contribute significantly to such a paradigm.
Rapid estimation of Brilliant Blue concentrations in soil by diffuse reflectance spectroscopy
Authors: Bogner Christina , Schmiedinger Iris , Huwe Bernd 
Published: July 2019

AbstractBrilliant Blue is often used to trace water movement in soils. Its concentration in soil samples is usually determined by extraction – a laborious procedure with varying accuracy. We show that Brilliant Blue can be estimated directly by visible diffuse reflectance spectroscopy. We build a PLSR (partial least squares regression) model for the concentration range of 0.1 to 15 mg Brilliant Blue per g soil with an RMSE (root mean square error of prediction) of 1 mg g-1 and an R2adj of 0.9. However, as the method is based on visible spectra, prediction accuracy can be altered by variations in soil colour between calibration and prediction data sets.
Evaluation of some cellular immune index in HIV infected participants
Authors: Ifeanyichukwu Martin , Meludu Sam , Ele Prince , Ukibe Nkiru , Onyenekwe Charles , Ezeani Michael , Ezechukwu Clement , Amilo Grace , Umeanaeto Pauline 
Published: July 2019

AbstractThe study was designed to evaluate some cellular immune index of HIV infected participants. For the study, 80 HIV infected participants were recruited for the study. They were aged 15 - 55 years. 45 of these participants were classified as Symptomatic HIV (Stage 11), while the remaining 35 were Asymptomatic HIV (Stage 1). Similarly, 40 HIV seronegative participants served as Control. Blood samples collected from the participants were used HIV screening and confirmation, CD4+ T cell count, absolute lymphocyte count and percent lymphocyte transformation. The CD4+T cell count and percent Lymphocyte Transformation count were significantly lowered in HIV infected participants compared with the HIV Seronegative participants (p&lt;0.05 in each case). Symptomatic HIV seropositive participants also presented with lowered CD4 and percent lymphocyte transformation, compared with the asymptomatic HIV participants (p&lt;0.05 in each case). The lowered CD4+T cell count suggests possible quantitative destruction of cellular immune cells (mainly Th1 cells). While the lowered percent blast formation in HIV infection indicates functional derangement of the cellular immune cells. Meanwhile no significant difference was observed in absolute lymphocyte count among the symptomatic, asymptomatic and control participants (p&gt; 0.05).
Sparse bayesian step-filtering for high-throughput analysis of molecular machine dynamics
Authors: Little Max , Jones Nick 
Published: July 2019

AbstractNature has evolved many molecular machines such as kinesin, myosin, and the rotary flagellar motor powered by an ion current from the mitochondria. Direct observation of the step-like motion of these machines with time series from novel experimental assays has recently become possible. These time series are corrupted by molecular and experimental noise that requires removal, but classical signal processing is of limited use for recovering such step-like dynamics. This paper reports simple, novel Bayesian filters that are robust to step-like dynamics in noise, and introduce an L1-regularized, global filter whose sparse solution can be rapidly obtained by standard convex optimization methods. We show these techniques outperforming classical filters on simulated time series in terms of their ability to accurately recover the underlying step dynamics. To show the techniques in action, we extract step-like speed transitions from Rhodobacter sphaeroides flagellar motor time series. Code implementing these algorithms available from http://www.eng.ox.ac.uk/samp/members/max/software/
Vitamin C insufficiency causes the stress-induced sudden death through the induction of extensive heart injury.
Authors: Kang Jae Seung , Kim Sung Joon , Bae Seyeon , Kong Joo Myung , Lee Na-Eun , Maeng Hyung Gun , Kim Yong Sung , Kim Hang Rae , Kim Hyemin , Kim Yong-Jin , Lee Seung-Pyo , Kim Kyung-Hee , Kim Daehee , Sohn Dae-Won , Cho Byung Joo , Hwang Young Il , Lee Wang Jae 
Published: July 2019

AbstractVitamin C scavenges toxic free radicals as an antioxidant, and oxidative stress is considered as a major contributor inducing damage to cardiomyocytes in heart diseases. Also, it is well-known that stress provokes oxidative stress and induces cardiac sudden death. Here we show the effects of vitamin C on the prevention of cardiac damage by stress in gulo(-/-) mice which cannot synthesize vitamin C. Vitamin C-insufficient gulo(-/-) mice under stress showed prominent cardiac damage and expired within 2 weeks. It was accompanied with structural changes in the heart, cardiac dysfunction and severe emphysema. These changes were caused by the elevation of pro-inflammatory cytokines, especially TNF-&x03B1;, the activation of MMP-2/MMP-9, an increase in oxidative stress and a remarkable decrease in noradrenaline production. Thus, vitamin C insufficiency causes extensive cardiac damage under stress through regulating cytokine and hormone production as well as redox homeostasis, which results in stress-induced sudden death.
Intrinsic Activity in the Fly Brain Gates Visual Information during Behavioral Choices
Authors: Tang Shiming , Juusola Mikko 
Published: July 2019

AbstractThe small insect brain is often described as an input/output system that executes reflex-like behaviours. It can also initiate neural activity and behaviours intrinsically, seen as spontaneous behaviours, different arousal states and sleep. However, little is known about how intrinsic activity in neural circuits affects sensory information processing in the insect brain and variability in behaviour. Here, by simultaneously monitoring Drosophila’s behavioural choices and brain activity in a flight simulator system, we identify intrinsic activity that is associated with the act of selecting between visual stimuli. We recorded neural output (multi-unit action potentials and local field potentials) in the left and right optic lobes of a tethered flying Drosophila, while its attempts to follow visual motion (yaw torque) were measured by a torque meter. We show that when facing competing motion stimuli on its left and right, Drosophila generate large torque responses that flip from side to side. The delayed onset (0.1-1 s) and spontaneous switch-like dynamics of these responses make this behaviour different from the classic steering reflexes. Drosophila, thus, seem to choose one stimulus at a time and attempt to rotate toward its direction. With this behaviour, the neural output of the optic lobes alternates; being augmented on the side chosen for body rotation and suppressed on the opposite side, even though the visual input to the fly eyes stays the same. Thus, the flow of information from the fly eyes seems gated intrinsically, with this process highlighting chosen information while ignoring the irrelevant. We propose that in small insect brains of limited capacity, intrinsic activity can play an important role in modulating neural information processing and behaviour.
Drosophila and human transcriptomic data mining provides evidence for therapeutic mechanism of pentylenetetrazole in Down syndrome
Authors: Sharma Abhay 
Published: July 2019

AbstractPentylenetetrazole (PTZ) has recently been found to ameliorate cognitive impairment in rodent models of Down syndrome (DS). The mechanism underlying PTZ’s therapeutic effect is however not clear. Microarray profiling has previously reported differential expression of genes in DS. No mammalian transcriptomic data on PTZ treatment however exists. Nevertheless, a Drosophila model inspired by rodent models of PTZ induced kindling plasticity has recently been described. Microarray profiling has shown PTZ’s downregulatory effect on gene expression in fly heads. In a comparative transcriptomics approach, I have analyzed the available microarray data in order to identify potential mechanism of PTZ action in DS. I find that transcriptomic correlates of chronic PTZ in Drosophila and DS counteract each other. A significant enrichment is observed between PTZ downregulated and DS upregulated genes, and a significant depletion between PTZ downregulated and DS dowwnregulated genes. Further, the common genes in PTZ downregulated and DS upregulated sets show enrichment for MAP kinase pathway. My analysis suggests that downregulation of MAP kinase pathway may mediate therapeutic effect of PTZ in DS. Existing evidence implicating MAP kinase pathway in DS supports this observation.
Why Intelligent People Live Longer
Authors: Hauser Robert , Palloni Alberto 
Published: July 2019

AbstractNumerous studies find a positive relationship between cognitive ability, IQ as measured in childhood or youth, and subsequent survival. Explanations range from the idea that low ability is an indicator of adverse systemic events in early life to the idea that high cognitive functioning is required continuously to maintain health and reduce threats to survival. The Wisconsin Longitudinal Study (WLS) has followed a large cohort of Wisconsin high school seniors from ages 18 to 69. As expected, in the WLS survival varies positively with adolescent IQ. However, rank in high school class accounts completely for the relationship between IQ and survival, and it has a much larger effect on survival. These findings suggest that cognitive functioning improves survival by promoting behaviours that boost health status, minimize exposure to known risks and optimize returns to health producing inputs, and that such behaviours are firmly in place by late adolescence.