bluuebunny/crossref_metadata_2025 huggingface dataset:
RIGHT ENGEL-TYPE SUBGROUPS AND LENGTH PARAMETERS OF FINITE GROUPS
Authors: KHUKHRO E. I. , SHUMYATSKY P. , TRAUSTASON G.
Published: July 2019

Let $g$ be an element of a finite group $G$ and let $R_{n}(g)$ be the subgroup generated by all the right Engel values $[g,_{n}x]$ over $x\in G$. In the case when $G$ is soluble we prove that if, for some $n$, the Fitting height of $R_{n}(g)$ is equal to $k$, then $g$ belongs to the $(k+1)$th Fitting subgroup $F_{k+1}(G)$. For nonsoluble $G$, it is proved that if, for some $n$, the generalized Fitting height of $R_{n}(g)$ is equal to $k$, then $g$ belongs to the generalized Fitting subgroup $F_{f(k,m)}^{\ast }(G)$ with $f(k,m)$ depending only on $k$ and $m$, where $|g|$ is the product of $m$ primes counting multiplicities. It is also proved that if, for some $n$, the nonsoluble length of $R_{n}(g)$ is equal to $k$, then $g$ belongs to a normal subgroup whose nonsoluble length is bounded in terms of $k$ and $m$. Earlier, similar generalizations of Baer’s theorem (which states that an Engel element of a finite group belongs to the Fitting subgroup) were obtained by the first two authors in terms of left Engel-type subgroups.
Dosimetric evaluation of two phases of respiratory movement using a lung equivalent material for radiotherapy treatment planning
Authors: Inal Aysun
Published: July 2019

Background/aim:

Radiation dosimetry requires special phantoms which are comparable with organs and tissues of a human body. The lung is one of the organs with a low density. Therefore, it is important to create and use lung equivalent phantoms in dosimetric controls. The aim of this study was to investigate the importance of using lung equivalent phantoms for different respiratory phases during measurements with both computed tomography (CT) and linear accelerator.

Materials and methods:

The maximum lung inhalation phantom (LIP) and lung exhalation phantom (LEP) were created for two respiratory phases. The Hounsfield Unit (HU) values based on the selected slice thickness and CT tube voltages were investigated, as well as the difference between energy and algorithms used in the treatment planning system.

Results:

It was found that the change in HU values according to slice thickness were more significant in measurements for respiratory phases. The dose difference between LEP and LIP at a point which is located 1 cm below the surface of the phantoms was found as 1·0% for 6 megavolt (MV) and 2·8% for 18 MV. The highest difference between the two algorithms was found to be 7·22% for 6 MV and 10·93% for 18 MV for LIP phantom.

Conclusion:

It can be said that the LIP and LEP phantoms prepared in accordance with respiratory phases can be a simple and inexpensive method to investigate any difference in dosimetry during respiratory phases. Also, measured and calculated dose values are in good agreement when thinner slice thickness was chosen.
Validation of the caregiver oncology quality of life questionnaire in Portuguese caregivers of myeloma patients
Authors: Pereira M. Graça , Vilaça Margarida , Pereira Marta , Bacalhau Rosário , Monteiro Sara , Fernandes Bruna , Faria Sara , Ferreira Gabriela
Published: July 2019

Objective

Cancer diagnosis affects patients, their families, and their caregivers in particular. This study focused on the validation of the CareGiver Oncology Quality of Life (CarGOQoL) questionnaire in Portuguese caregivers of patients with multiple myeloma, from the caregiver's point of view.

Method

This was a cross-sectional study with 146 caregivers of patients with multiple myeloma from outpatient medical oncology and clinical hematology consultations from five hospitals in north and central Portugal. Participants were assessed on quality of life (QoL), psychological morbidity and social support.

Result

The Portuguese version maintains 17 of the original 29 items version, maintaining general coherence and a dimensional structure that is clinically interpretable. Reliability findings indicated good internal consistency for the total scale (0.86) and respective subscales (0.75 to 0.88), which is in agreement with the alpha values from the previous CarGOQoL validation study for the corresponding subscales (0.74 to 0.89) and total scale (0.90).

Significance of results

The CarGOQoL is a reliable and valid tool for clinical trials and intervention programs to assess QoL in caregivers of myeloma patients. Future studies should validate the adapted version in caregivers of other types of cancer patients including other chronic diseases.
Modifications of active phased antenna arrays near-field diagnosis method based on compressive sensing
Authors: Kuznetsov Grigory , Temchenko Vladimir , Miloserdov Maxim , Voskresenskiy Dmitry
Published: July 2019

This paper presents two modifications of compressive sensing (CS)-based approach applied to the near-field diagnosis of active phased arrays. CS-based antenna array diagnosis allows a significant reduction of measurement time, which is crucial for the characterization of electrically large active antenna arrays, e.g. used in synthetic aperture radar. However, practical implementation of this method is limited by two factors: first, it is sensitive to thermal instabilities of the array under test, and second, excitation reconstruction accuracy strongly depends on the accuracy of the elements of the measurement matrix. First proposed modification allows taking into account of thermal instability of the array by using an iterative ℓ1-minimization procedure. The second modification increases the accuracy of reconstruction using several simple additional measurements.
Effects of Fault Roughness on Coseismic Slip and Earthquake Locations
Authors: Allam A. A. , Kroll K. A. , Milliner C. W. D. , Richards‐Dinger K. B.
Published: July 2019

Fault zone structure is well known to exert strong controls on earthquake properties including coseismic slip distribution, rupture propagation direction, and hypocenter location. It has also been well established that the principal slip surface, which accommodates the majority of earthquake displacement, exhibits roughness at all scales following self‐affine fractal distributions. Here we explore the relationship between fault roughness and specific earthquake properties including coseismic slip distribution and hypocenter location based on long‐term simulations of earthquake catalogs on fractally rough faults. We begin by using the von Kármán autocorrelation function to procedurally generate single faults with different fractal roughness properties, which we place in a homogeneous elastic solid and apply pure right‐lateral shear at a constant back slip rate with the earthquake simulator RSQSim. Running the simulations for 10,000 years each, we generate millions of earthquakes including thousands of events with Mw > 6.0, which rupture the surface. We show that the patterns of surface rupture in these large events follow self‐affine fractal distributions with consistent fractal dimension related distinctly to the fractal dimension of the fault. In addition, the hypocenters of these large events occur in very specific predictable locations where the longest wavelength structure produces a stress asperity (i.e., restraining bend). The resulting patterns can explain many features observed on real fault systems, including clustered hypocenter locations, spatially variable coseismic slip distributions, and characteristic slip recurrence behavior. These results demonstrate a quantitative link between a directly measurable fault property—roughness—and the properties of future earthquakes.
Characteristics of Ground Motion Generated by Wind Interaction With Trees, Structures, and Other Surface Obstacles
Authors: Johnson Christopher W. , Meng Haoran , Vernon Frank , Ben‐Zion Yehuda
Published: July 2019

Analysis of continuous seismic waveforms from a temporary deployment at Sage Brush Flats on the San Jacinto fault reveals earthquake‐ and tremor‐like signals generated by the interaction of wind with obstacles above the surface. Tremor‐like waveforms are present at the site during wind velocities above 2 m/s, which occur for 70% of the deployment duration. The response to the wind has significant spatial variability with highest ground motions near large surface objects. The wind‐related signals show ground velocities that exceed the average ground motions of M1.0–1.5 earthquakes for 6–31% of the day. Waveform spectra indicate a modulation of amplitude that correlates with wind velocity and distance from local structures. Earthquake‐like signals are found to originate from local structures and vegetation, and are modified on length scales of tens of meters. Transient signals originating beyond the study area are also observed with amplitudes greater than some microseismic events. The wind‐related ground motions contribute to local high‐frequency seismic noise. Some of these signals may be associated with small failures of the subsurface material. During elevated wind conditions a borehole seismometer at a depth of 148 m shows increased energy in the 1–8‐Hz band that is commonly used for earthquake and tremor detection. The wind‐related earthquake‐ and tremor‐like signals should be accounted for in earthquake detection algorithms due to the similar features in both time and frequency domains. Proper recognition of wind‐related ground motions can contribute to understanding the composition of continuous seismic waveforms and characterize mechanical properties of the shallow crust.
Testing the Amplitude of the Deconvolution‐Based Ambient Field Green's Functions by 3‐D Simulations of Elastic Wave Propagation in Sedimentary Basins
Authors: Nie Shiying , Anthony David , Ma Shuo
Published: July 2019

We test the amplitude of deconvolution‐based ambient field Green's functions in 3‐D numerical simulations of seismic wave propagation. We first simulate strongly scattered waves in a hypothetical 3‐D sedimentary basin with small‐scale heterogeneities, which provides an ideally random environment to test various approaches of extracting the amplitude of Green's functions, as the deterministic station‐to‐station Green's functions can be computed in the given velocity structure. Our second model computes the station‐to‐station Green's functions in the Community Velocity Model (S4.26) for Southern California and compares them with the Green's functions extracted from 1 year of ambient noise data. In both models, remarkable waveform similarity among different Green's functions is obtained. In the hypothetical basin model where the wavefield is nearly random, both the correlation‐ and deconvolution‐based Green's functions contain robust amplitude information. However, large‐amplitude biases are observed in the Green's functions extracted from ambient noise in Southern California, showing a strong azimuthal dependence. The deconvolution approach in general overestimates the amplitude along the direction of noise propagation but underestimates it in other azimuths. The correlation approach with temporal normalization and spectral whitening generates similar amplitude to the deconvolution in a wide azimuthal range. Our results corroborate that the inhomogeneous distribution of noise sources biases the amplitude of Green's functions. Carefully reducing these biases is necessary to use these ambient field Green's functions in the virtual earthquake approach.
Understanding the Terrestrial Effects of Arctic Sea Ice Decline
Authors: Vincent Warwick , Can�rio Jo�o , Boike Julia
Published: July 2019

T-MOSAiC Workshop 2019; Arkhangelsk, Russia, 25–26 May 2019
Uncontrolled Chemical Releases: A Silent, Growing Threat
Authors: Miner K.
Published: July 2019

Uncontrolled releases of household, industrial, and agricultural chemicals during natural disasters pose an underappreciated hazard to humans and ecosystems. Here’s what we can do.
Role of the porous structure of the bioceramic scaffolds in bone tissue engineering
Authors: Zhen Wang , Jiang Chang , Feng Bai , Xiaojiang Sun , Jianxi Lu , Li Lin , Chen Lei , Rong Dai
Published: July 2019

The porous structure of biomaterials plays a critical role in improving the efficiency of biomaterials in tissue engineering. Here we fabricate successfully porous bioceramics with accurately controlled pore parameters, and investigate the effect of pore parameters on the mechanical property, the cell seeding proliferation and the vascularization of the scaffolds. This study shows that the porosity play an important role on the mechanical property of the scaffolds, which is affected not only by the macropores size, but also by the interconnections of the scaffolds. Larger pores are beneficial for cell growth in scaffolds. In contrast, the interconnections do not affect cell growth much. The interconnections appear to limit the number of blood vessels penatrating through adjacent pores, and both the pores size and interconnections can determine the size of blood vessels. The results may be referenced on the selective design of porous structure of biomaterials to meet the specificity of biological application.
Interaction of the TNFR-receptor associated factor TRAF1 with I-kappa B kinase 2 (IKK2, IKK-beta, IKBKB) and TRAF2 indicating a dose dependent regulatory function of TRAF1 for NF-kappa B signaling
Authors: Schmid Johannes , Birbach Andreas
Published: July 2019

IKK2 is one of the most crucial signaling kinases for activation of the transcription factor NF-kappa B. Since many NF-kappa B activating pathways converge at the level of IKK2, we searched for interaction partners of this kinase using the C-terminal part (aa 466-756) as bait in a yeast two-hybrid system. We identified the N-terminal part (aa 1-228) of the TNF-receptor associated factor TRAF1 as putative interaction partner, which was subsequently confirmed in mammalian cells by coimmunoprecipitation experiments. However, this interaction seemed weaker than the interaction between TRAF1 and TRAF2, an important activating adapter molecule of NF-kappa B signaling indicating that relative levels of IKK2, TRAF1 and TRAF2 might be important for the final biological readout. Reporter gene and kinase assays using ectopic expression of TRAF1 indicated that it can have both activating and inhibiting functions for IKK2 and NF-kappa B. Co-expression of fluorescently tagged TRAF1 and TRAF2 at different ratios implied that TRAF1 can affect clustering and presumably the activating function of TRAF2 in a dose dependent manner.
Traditional wisdom confirmed by scientific research: Jatropha species from Mexico is non-toxic
Authors: Makkar Harinder , Kumar Vikas , Oyeleye Olubisi , Akinleye Akinwale Oluwasegun , Angulo-Escalante Miguel , Becker Klaus
Published: July 2019

The seeds of Jatropha platyphylla, available on the pacific coast from Sinaloa to Michoacán including the Nayarit and Jalisco states in Mexico, are consumed by local communities after roasting them in a manner similar to that used for peanuts. The kernels and kernel meal of J. platyphylla were found to be free of phorbol esters but the kernel meal contained antinutritional factors: trypsin inhibitor, lectins and phytate at levels similar to those in J. curcas kernel meal. However, trypsin inhibitor and lectins are heat labile so this explains why the local people can eat roasted seeds without ill effect. The fatty acid profile of J. platyphylla oil was similar to that of J. curcas and the kernels of both these species contained ca 58% oil. The crude protein content of J. platyphylla kernel meal was 75% against 60% in J. curcas, and the amino acid compositions were similar. All the essential amino acids, except lysine, were more abundant than, or comparable to those, in soybean meal or the FAO Reference protein. Tilapia and other fish species have been found to be particularly sensitive to Jatropha toxins. For this reason they are useful subjects for bioassays. The heated J. platyphylla kernel meal was included in a standard diet (crude protein 36%) for Nile tilapia (Oreochromis niloticus) to replace 50% of the fish meal protein. The fish grew as well as those on a control diet in which none of the fish meal was replaced and those on a diet in which 50% of the fish meal protein was replaced by soybean meal. In all the three groups, blood biochemical parameters that serve as biomarkers for toxicity were within the normal ranges. This study confirmed the non-toxic nature of J. platyphylla. The kernels and kernel meal of this species could help alleviate protein and energy deficiency in malnourished children in the lower mountain skirts of pacific coastal areas of Mexico. It could also be used to produce new cultivars with desirable traits using conventional inter species cross breeding and molecular breeding techniques.
Skin Typing and High Resolution MRI of Human Skin: Multiple Contrast Approach for Image Characterization
Authors: Sharma Rakesh
Published: July 2019

Background and objectives:

The ex vivo magnetic resonance microimaging (MRM) image characteristics are reported in human skin excised samples. Design and methods:Human excised skin samples were imaged using custom coil placed inside 500 MHz NMR imager for high resolution microimaging. Skin in vivo- and ex vivo MRI images were processed for characterization of different skin structures. Contiguous cross-sectional T1-weighted 3D spin echo MRI, T2-weighted 3D spin echo MRI and proton density images were compared with skin histopathology and NMR peaks. In all skin specimens, epidermis and dermis thickening and hair follicle size was measured using MRM. Results: Optimized TE and TR parameters and multicontrast enhancement generated better MRI visibility of different skin components. Within high MR signal regions near to custom coil, MRI images at short echo time were comparable with digitized histological sections for skin structures of epidermis, dermis, hair follicles in 6 (67%) of the 9 specimens from different age groups. Skin % tissue composition, measurement of epidermis, dermis, sebaceous gland and hair follicle size, skin NMR peaks were signatures of skin type. The image processing determined the dimensionality of skin tissue components and skin typing in different age groups. Conclusion: The ex vivo MRI images and histopathology of skin may measure the skin structures and skin NMR peaks with image processing may be tool for determining skin age typing and skin composition.
The hypothesis of basic phenotype modules
Authors: von Zelewsky Thomas
Published: July 2019

The 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

Autism 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

A 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

The 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

Evidence 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

A 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

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

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

A 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

Brilliant 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

The 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<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<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> 0.05).
Sparse bayesian step-filtering for high-throughput analysis of molecular machine dynamics
Authors: Little Max , Jones Nick
Published: July 2019

Nature 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

Vitamin 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

The 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

Pentylenetetrazole (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

Numerous 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.
The largest reservoir of mitochondrial introns is a relic of an ancestral split gene
Authors: Ferandon Cyril , Moukha Serge , Callac Philippe , Benedetto Jean-Pierre , Castroviejo Michel , Barroso Gerard
Published: July 2019

In eukaryotes, introns are located in nuclear and organelle genes from several kingdoms (ref. 1-4). Large introns (0.1 to 5 kbp) are frequent in mitochondrial genomes of plant and fungi (ref. 1,5) but scarce in Metazoa, despite these organisms are grouped with fungi among Opisthokonts. Introns are classified in two main groups (I and II) according to their RNA secondary structure involved in the intron self-splicing mechanism (ref. 5,6). Most of the group I introns carry a "Homing Endonuclease Gene" (ref. 7-9) encoding a DNA endonuclease acting in the transfer and site specific integration "homing") and allowing the intron spreading and gain after lateral transfer even between species from different kingdoms (ref. 10,11). Opposite to this "late intron" paradigm, the "early intron" theory indicates that introns, which would have been abundant in the ancestral genes, would mainly evolve by loss (ref. 12,13).Here we report the sequence of the cox1 gene of the button mushroom Agaricus bisporus, the most worldwide cultivated mushroom. This gene is both the longest mitochondrial gene (29,902 nt) and the largest Group I intron reservoir reported to date. An analysis of the group I introns available in cox1 genes shows that they are ancestral mobile genetic elements, whose frequent events of loss (according to the "late theory") and gain by lateral transfer ("early theory") must be combined to explain their wide and patchy distribution extending on several kingdoms. This allows the conciliation of the "early" and "late intron" paradigms, which are still matters of much debate (ref. 14,15). The overview of the intron distribution indicates that they evolve towards elimination. In such a landscape of eroded and lost intron sequences, the A. bisporus largest intron reservoir, by its singular dynamics of intron keeping and catching, constitutes the most fitted relic of an early split gene.
Is severity of clinical manifestations following H. lepturus envenomation related to serum TNF-α level?
Authors: Jalali Amir , Pipelzadeh Mohammad , Taraz Mohammad , Khodadadi Ali , Makvandi Manoochr
Published: July 2019

Thirty six patients, with varying degrees of severity of envenomation, because of envenomation by Hemiscorpius lepturus scorpion, were systematically investigated. The serum levels (by double-ligand ELIZA kit) of interlukin-1 (IL-1), interlukin-6 (IL-6), interlukin-8 (IL-8) and tumor necrosis factor-α (TNF- α) were compared with 30 healthy controls and 10 age-matched patients envenomed by Mesobuthus eupeus scorpion. Blood samples from M. eupeus and H. lepturus victims were taken on admission and once more after 6 hr after serotherapy with multivalent antivenom from H. lepturus envenomed subjects. The results suggest that, unlike M. eupeus, the toxic manifestations observed following H lepturus may be associated with increase in serum TNF-α level and are positively correlated with its severity.
The model of proteolysis
Authors: Dittwald Piotr , Gambin Anna
Published: July 2019

This document presents the original approach for estimating parameters of proteolysis process. Data used to fit the model are taken from massspectrometric experiments. For parameters estimation the Levenberg-Marquadt algorithm is used. The motivation for model is a hypothesisthat discrimination between cancer patients and healthy donors can be based on activity of peptide cleaving enzymes (i.e. peptidases).
p53 Response to DNA Damage in S-phase
Authors: Reisman David , Takahashi Paula , Polson Amanda
Published: July 2019

p53 induces the transcription of genes that negatively regulate progression of the cell cycle in response to DNA damage or other cellular stressors, and thus participates in maintaining genome stability. Under stress conditions, p53 must be activated to prohibit the replication of cells containing damaged DNA. However, in normal, non-stressed cells, p53 activity must be inhibited. Previous studies have demonstrated that p53 transcription is activated before or during early S-phase in cells progressing from G0/G1 into S-phase. In that this is not what would be predicted from a gene involved in growth arrest and apoptosis, in this study, we provide evidence that this induction occurs to provide available p53 mRNA in order to prepare the cell for DNA damage in S-phase, ensuring a rapid response to DNA damage before exiting this stage. When comparing exponential to synchronized Swiss3T3 cells upon Camptothecin-induced DNA damage, we found that in synchronized cells, p53 protein levels increased earlier, Bax and p21 transcription was activated earlier and to a greater extent and apoptosis occurred earlier and to a greater extent. These findings are consistent with p53 transcription being induced in S-phase to provide for a rapid DNA-damage response during S-phase of the cell cycle.
Genome Structural-Functional Peculiarities Affecting Plant Epigenetic Variability and Evolution
Authors: Levites Evgenii
Published: July 2019

There is an attempt to explain some evolutionary processes in plants such as saltatory changes on the base of multidimensionality of plant inherited information coding. According to the suggested hypothesis, inherited information is coded by not only a nucleotide sequence but also by chromosome differential endoreduplication. It is supposed that chromosomes compete among each other for the contact with the nuclear membrane, but a change in the endoreduplication degree of various chromosome sites can result in a change of a competition ability for the contact with a nuclear membrane. A simultaneous increase of chromosome endoreduplication degree of many sites can lead to an increase of nuclear membrane surface and to a change in chromosome competitive interrelations and, respectively, to a change of activity of many genes. Phenotypicaly it may manifest itself as a saltatory change of many traits.
Prolonged maturation of prefrontal white matter in chimpanzees
Authors: Sakai Tomoko , Hirai Daichi , Mikami Akichika , Suzuki Juri , Hamada Yuzuru , Tomonaga Masaki , Tanaka Masayuki , Miyabe-Nishiwaki Takako , Makishima Haruyuki , Nakatsukasa Masato , Matsuzawa Tetsuro
Published: July 2019

Delayed maturation in the prefrontal cortex, a brain region associated with complex cognitive processing, has been proposed to be specific to humans. However, we found, using a longitudinal design, that prefrontal white matter volume in chimpanzees increased gradually with age, and the increase appears to continue beyond the onset of puberty, as in humans. This provides the first evidence for a prolonged period of prefrontal connection elaboration in great apes.